Hi Brad, I am cc'ing this to the chimera list. I think that you should write a python script to run DOCK prep on the command line. See the following: http://www.cgl.ucsf.edu/pipermail/chimera-dev/2011/000784.html For other example scripts see the following: http://www.cgl.ucsf.edu/pipermail/chimera-users/2009-February/003539.html You should not have to specify the AMBERHOME path. This is done internally to chimera. as an aside, It is unnecessary to run antichamber with sudo. I hope this helps, Trent E. Balius Graduate Student, Rizzo Group, Department of Applied Mathematics and Statistics, Stony Brook University. Office: Math Tower 3-129, Phone: (631) 632-8519 URL: http://www.ams.sunysb.edu/~tbalius/ -----Original Message----- From: Brad Ridder <clustro@gmail.com> To: dock-fans <dock-fans@docking.org> Sent: Wed, Feb 29, 2012 4:38 pm Subject: [Dock-fans] Help with antechamber Hi Dockfans, My name is Brad; I am a grad student in the dept. of chemical engineering at Purdue University. We are experimenting with DOCK for various drug discovery work. At the moment, I am trying to do execute all of the "dock prep" commands through the Terminal, since it is not practical to do large volumes of Dock Prep by hand through the CHIMERA GUI. Corresponding to what is in the DOCK tutorial, I am on "Receptor and Ligand Preparation." I got reduce to work, in order to add hydrogens. Now, I am trying to get antechamber to work, in order to add the charges, but it is not working. Here is the command I am running: sudo ./antechamber -i $DESKTOP/3GLR.pdb -fi pdb -o $DESKTOP/3GLRcharged.mol2 -fo mol2 Which returns the error: Warning: $AMBERHOME and $DOCK_HOME enviornment strings are not set, use "mopac.sh" in the work directory Cannot open CONNECT.TPL , exit The atom number exceeds the MAXATOM, reallocate memory I looked around in the dock6 directory, and found a folder called "parameters/antechamber", which contains CONNECT.TPL. I figured this is what should be the $AMBERHOME directory. For DOCK_HOME, I figured it should be the dock6 folder. Here is what I have in my .bash_profile file in my home folder. export AMBERHOME='/home/.../DOCK6.5/dock6/parameters/antechamber' export DOCK_HOME='/home/.../DOCK6.5/dock6' I also tried using the "amber11" folder that comes with CHIMERA as AMBERHOME, but to no effect. I don't actually have AMBER installed on my computer, but since CHIMERA can add charges without actually requiring the purchase of AMBER, I do not think that is the problem. I did not know what to do with "mopac.sh." I ran the script, but it says it needs input files. What am I doing wrong that is preventing antechamber from executing correctly? -- Bradley James Ridder Chakrabarti Group Graduate Student School of Chemical Engineering Purdue University _______________________________________________ Dock-fans mailing list Dock-fans@docking.org http://mailman.docking.org/mailman/listinfo/dock-fans
This previous posting to the dock-fans list seems to be more directly pertinent: http://mailman.docking.org/pipermail/dock-fans/2007-May/001043.html --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu On Feb 29, 2012, at 2:47 PM, Trent E. Balius wrote:
Hi Brad,
I am cc'ing this to the chimera list.
I think that you should write a python script to run DOCK prep on the command line. See the following:
http://www.cgl.ucsf.edu/pipermail/chimera-dev/2011/000784.html
For other example scripts see the following:
http://www.cgl.ucsf.edu/pipermail/chimera-users/2009-February/003539.html
You should not have to specify the AMBERHOME path. This is done internally to chimera.
as an aside, It is unnecessary to run antichamber with sudo.
I hope this helps,
Trent E. Balius Graduate Student, Rizzo Group, Department of Applied Mathematics and Statistics, Stony Brook University. Office: Math Tower 3-129, Phone: (631) 632-8519 URL: http://www.ams.sunysb.edu/~tbalius/
-----Original Message----- From: Brad Ridder <clustro@gmail.com> To: dock-fans <dock-fans@docking.org> Sent: Wed, Feb 29, 2012 4:38 pm Subject: [Dock-fans] Help with antechamber
Hi Dockfans,
My name is Brad; I am a grad student in the dept. of chemical engineering at Purdue University.
We are experimenting with DOCK for various drug discovery work. At the moment, I am trying to do execute all of the "dock prep" commands through the Terminal, since it is not practical to do large volumes of Dock Prep by hand through the CHIMERA GUI.
Corresponding to what is in the DOCK tutorial, I am on "Receptor and Ligand Preparation." I got reduce to work, in order to add hydrogens.
Now, I am trying to get antechamber to work, in order to add the charges, but it is not working. Here is the command I am running:
sudo ./antechamber -i $DESKTOP/3GLR.pdb -fi pdb -o $DESKTOP/ 3GLRcharged.mol2 -fo mol2
Which returns the error:
Warning: $AMBERHOME and $DOCK_HOME enviornment strings are not set, use "mopac.sh" in the work directory
Cannot open CONNECT.TPL , exit The atom number exceeds the MAXATOM, reallocate memory
I looked around in the dock6 directory, and found a folder called "parameters/antechamber", which contains CONNECT.TPL. I figured this is what should be the $AMBERHOME directory. For DOCK_HOME, I figured it should be the dock6 folder.
Here is what I have in my .bash_profile file in my home folder.
export AMBERHOME='/home/.../DOCK6.5/dock6/parameters/antechamber' export DOCK_HOME='/home/.../DOCK6.5/dock6'
I also tried using the "amber11" folder that comes with CHIMERA as AMBERHOME, but to no effect.
I don't actually have AMBER installed on my computer, but since CHIMERA can add charges without actually requiring the purchase of AMBER, I do not think that is the problem.
I did not know what to do with "mopac.sh." I ran the script, but it says it needs input files.
What am I doing wrong that is preventing antechamber from executing correctly?
-- Bradley James Ridder Chakrabarti Group Graduate Student School of Chemical Engineering Purdue University
_______________________________________________ Dock-fans mailing list Dock-fans@docking.org http://mailman.docking.org/mailman/listinfo/dock-fans _______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
Hi, Here's another similar ligand prep script: http://mailman.docking.org/pipermail/dock-fans/2011-December/002591.html While it is a good pedagogical exercise to prep once manually, scripting is the only practical approach for lots of ligands. As far as running antechamber, be careful and be specific about which one you run: If you are manually running Dock's antechamber then define DOCK_HOME. Do not define AMBERHOME. See http://dock.compbio.ucsf.edu/DOCK_6/faq.htm#Error%20from%20amberize_ligand; If you are manually running Chimera's antechamber then DOCK_HOME is irrelevant but AMBERHOME may be relevant. ( I have not manually run Chimera's antechamber, so my advice may be wrong. ) Also note that Dock's antechamber is circa 2006 with some key subsequent bugfixes. Chimera's antechamber is much more recent. Dock's antechamber uses mopac for qm; Chimera's antechamber uses sqm for qm; (http://ambermd.org/#AmberTools) I have found mopac to be more robust than sqm. Your mileage may vary. scott On Wed, Feb 29, 2012 at 04:08:22PM -0800, Eric Pettersen wrote:
This previous posting to the dock-fans list seems to be more directly pertinent:
http://mailman.docking.org/pipermail/dock-fans/2007-May/001043.html
On Feb 29, 2012, at 2:47 PM, Trent E. Balius wrote:
I am cc'ing this to the chimera list.
I think that you should write a python script to run DOCK prep on the command line. See the following:
http://www.cgl.ucsf.edu/pipermail/chimera-dev/2011/000784.html
For other example scripts see the following:
http://www.cgl.ucsf.edu/pipermail/chimera-users/2009-February/003539.html
You should not have to specify the AMBERHOME path. This is done internally to chimera.
as an aside, It is unnecessary to run antichamber with sudo.
-----Original Message----- From: Brad Ridder <clustro@gmail.com> To: dock-fans <dock-fans@docking.org>
My name is Brad; I am a grad student in the dept. of chemical engineering at Purdue University.
We are experimenting with DOCK for various drug discovery work. At the moment, I am trying to do execute all of the "dock prep" commands through the Terminal, since it is not practical to do large volumes of Dock Prep by hand through the CHIMERA GUI.
Corresponding to what is in the DOCK tutorial, I am on "Receptor and Ligand Preparation." I got reduce to work, in order to add hydrogens.
Now, I am trying to get antechamber to work, in order to add the charges, but it is not working. Here is the command I am running:
sudo ./antechamber -i $DESKTOP/3GLR.pdb -fi pdb -o $DESKTOP/ 3GLRcharged.mol2 -fo mol2
Which returns the error:
Warning: $AMBERHOME and $DOCK_HOME enviornment strings are not set, use "mopac.sh" in the work directory
Cannot open CONNECT.TPL , exit The atom number exceeds the MAXATOM, reallocate memory
I looked around in the dock6 directory, and found a folder called "parameters/antechamber", which contains CONNECT.TPL. I figured this is what should be the $AMBERHOME directory. For DOCK_HOME, I figured it should be the dock6 folder.
Here is what I have in my .bash_profile file in my home folder.
export AMBERHOME='/home/.../DOCK6.5/dock6/parameters/antechamber' export DOCK_HOME='/home/.../DOCK6.5/dock6'
I also tried using the "amber11" folder that comes with CHIMERA as AMBERHOME, but to no effect.
I don't actually have AMBER installed on my computer, but since CHIMERA can add charges without actually requiring the purchase of AMBER, I do not think that is the problem.
I did not know what to do with "mopac.sh." I ran the script, but it says it needs input files.
What am I doing wrong that is preventing antechamber from executing correctly?
Hi Eric, I tried the dockprep.py file you pointed to me a few emails ago. It seems like its exactly what I am looking for. The only problem is I get an error at the moment; I also have two other questions about it. ep.py file you pointed to me a few emails ago. It seems like its exactly what I am looking for. The only problem is I get an error at the moment; I also have two other questions about it. Here is the command I used: ./chimera --nogui pdb:2h4f $DESKTOP/dockprep.py The program then returns a bunch of text on what its doing. When adding the charges to the ligands with the AM1-BCC method is when the error pops up. Here is the (slightly abridged) error message, plus a few lines back: *Running ANTECHAMBER for residue NAD Running ANTECHAMBER command: /home/abhay/Desktop/rcg-research/personal-work/CHIMERA/bin/amber11/bin/antechamber -ek qm_theory='AM1', grms_tol=0.02, tight_p_conv=0, scfconv=1.d-10, -i /tmp/tmplP08co/ante.in.mol2 -fi mol2 -o /tmp/tmplP08co/ante.out.mol2 -fo mol2 -c bcc -nc -1 -j 5 -s 2 (NAD) Total number of electrons: 344; net charge: -1 (NAD) Running: /home/abhay/Desktop/rcg-research/personal-work/CHIMERA/bin/amber11/bin/sqm -O -i sqm.in -o sqm.out (NAD) Error: cannot run "/home/abhay/Desktop/rcg-research/personal-work/CHIMERA/bin/amber11/bin/sqm -O -i sqm.in -o sqm.out" of bcc() in charge.c properly, exit (NAD) Running: /home/abhay/Desktop/rcg-research/personal-work/CHIMERA/bin/amber11/bin/bondtype -j part -i ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac (NAD) Running: /home/abhay/Desktop/rcg-research/personal-work/CHIMERA/bin/amber11/bin/atomtype -i ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff Error while processing /home/abhay/Desktop/dockprep.py: Failure running ANTECHAMBER for residue NAD Check reply log for details* I am not sure what the problem is. $AMBERHOME and $DOCK_HOME are not defined, but that only seemed to cause problems before. Perhaps they need to be defined now? I would give you the reply log, but I don't know how to find it. I tried using: $ ./chimera --start Reply_Log --nogui pdb:2h4f $DESKTOP/dockprep.py I also tried reply_log, Reply_log, reply_Log, ReplyLog, replyLog, Replylog, and transposing --start and --nogui. None of those worked either. The program immediately returns: *Starting extension 'Reply_Log' failed* (or whatever the pertinent permutation of "reply_log" happens to be.) Assuming this can be fixed easily, I have one more question: this appears to only prepare the receptor for docking. What about prepping the ligand? Does that need its own new script? Thank you so much for your help, -Brad On Wed, Feb 29, 2012 at 7:08 PM, Eric Pettersen <pett@cgl.ucsf.edu> wrote:
This previous posting to the dock-fans list seems to be more directly pertinent:
http://mailman.docking.org/pipermail/dock-fans/2007-May/001043.html
--Eric
Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu
On Feb 29, 2012, at 2:47 PM, Trent E. Balius wrote:
Hi Brad,
I am cc'ing this to the chimera list.
I think that you should write a python script to run DOCK prep on the command line. See the following:
http://www.cgl.ucsf.edu/pipermail/chimera-dev/2011/000784.html
For other example scripts see the following:
http://www.cgl.ucsf.edu/pipermail/chimera-users/2009-February/003539.html
You should not have to specify the AMBERHOME path. This is done internally to chimera.
as an aside, It is unnecessary to run antichamber with sudo.
I hope this helps,
Trent E. Balius Graduate Student, Rizzo Group, Department of Applied Mathematics and Statistics, Stony Brook University. Office: Math Tower 3-129, Phone: (631) 632-8519 URL: http://www.ams.sunysb.edu/~tbalius/
-----Original Message----- From: Brad Ridder <clustro@gmail.com> To: dock-fans <dock-fans@docking.org> Sent: Wed, Feb 29, 2012 4:38 pm Subject: [Dock-fans] Help with antechamber
Hi Dockfans,
My name is Brad; I am a grad student in the dept. of chemical engineering at Purdue University.
We are experimenting with DOCK for various drug discovery work. At the moment, I am trying to do execute all of the "dock prep" commands through the Terminal, since it is not practical to do large volumes of Dock Prep by hand through the CHIMERA GUI.
Corresponding to what is in the DOCK tutorial, I am on "Receptor and Ligand Preparation." I got reduce to work, in order to add hydrogens.
Now, I am trying to get antechamber to work, in order to add the charges, but it is not working. Here is the command I am running:
*sudo ./antechamber -i $DESKTOP/3GLR.pdb -fi pdb -o $DESKTOP/3GLRcharged.mol2 -fo mol2*
Which returns the error: * Warning: $AMBERHOME and $DOCK_HOME enviornment strings are not set, use "mopac.sh" in the work directory
Cannot open CONNECT.TPL , exit The atom number exceeds the MAXATOM, reallocate memory*
I looked around in the dock6 directory, and found a folder called "parameters/antechamber", which contains CONNECT.TPL. I figured this is what should be the $AMBERHOME directory. For DOCK_HOME, I figured it should be the dock6 folder.
Here is what I have in my .bash_profile file in my home folder.
*export AMBERHOME='/home/.../DOCK6.5/dock6/parameters/antechamber' export DOCK_HOME='/home/.../DOCK6.5/dock6'*
I also tried using the "amber11" folder that comes with CHIMERA as AMBERHOME, but to no effect.
I don't actually have AMBER installed on my computer, but since CHIMERA can add charges without actually requiring the purchase of AMBER, I do not think that is the problem.
I did not know what to do with "mopac.sh." I ran the script, but it says it needs input files.
What am I doing wrong that is preventing antechamber from executing correctly?
-- Bradley James Ridder Chakrabarti Group Graduate Student School of Chemical Engineering Purdue University
_______________________________________________ Dock-fans mailing listDock-fans@docking.orghttp://mailman.docking.org/mailman/listinfo/dock-fans
_______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
-- Bradley James Ridder Chakrabarti Group Graduate Student School of Chemical Engineering Purdue University
Hi Brad, Well, a few things: 1) From your output I can tell that you are using an old version of Chimera. You should upgrade to the latest version (1.6.1) which includes a more recent version of antechamber with latest bug fixes. 2) I cannot get Chimera to fail on NAD (including old versions of Chimera). Does DockPrep work if you use it on 2h4f in regular, non-"nogui" mode? How about if you use it on 2gbp? Also, do you even want NAD present in the receptor when you attempt docking? 3) You couldn't possibly bring up the reply log in nogui mode since it creates a window. It's irrelevant anyway since the reply log output is the stuff you are already seeing on standard output (it only goes into the reply log in gui mode). For posterity, the syntax you would have used to start the reply log is: --start "Reply Log". 4) You would likely prep the ligand separately, yes. I am taking chimera-users off the reply-to for this, since I doubt most subscribers will be interested in the minutiae of this problem. --Eric On Mar 16, 2012, at 12:35 PM, Brad Ridder wrote:
Hi Eric,
I tried the dockprep.py file you pointed to me a few emails ago. It seems like its exactly what I am looking for. The only problem is I get an error at the moment; I also have two other questions about it.
ep.py file you pointed to me a few emails ago. It seems like its exactly what I am looking for. The only problem is I get an error at the moment; I also have two other questions about it.
Here is the command I used:
./chimera --nogui pdb:2h4f $DESKTOP/dockprep.py
The program then returns a bunch of text on what its doing. When adding the charges to the ligands with the AM1-BCC method is when the error pops up. Here is the (slightly abridged) error message, plus a few lines back:
Running ANTECHAMBER for residue NAD Running ANTECHAMBER command: /home/abhay/Desktop/rcg-research/ personal-work/CHIMERA/bin/amber11/bin/antechamber -ek qm_theory='AM1', grms_tol=0.02, tight_p_conv=0, scfconv=1.d-10, -i / tmp/tmplP08co/ante.in.mol2 -fi mol2 -o /tmp/tmplP08co/ante.out.mol2 - fo mol2 -c bcc -nc -1 -j 5 -s 2
(NAD) Total number of electrons: 344; net charge: -1
(NAD) Running: /home/abhay/Desktop/rcg-research/personal-work/ CHIMERA/bin/amber11/bin/sqm -O -i sqm.in -o sqm.out
(NAD) Error: cannot run "/home/abhay/Desktop/rcg-research/personal- work/CHIMERA/bin/amber11/bin/sqm -O -i sqm.in -o sqm.out" of bcc() in charge.c properly, exit
(NAD) Running: /home/abhay/Desktop/rcg-research/personal-work/ CHIMERA/bin/amber11/bin/bondtype -j part -i ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac
(NAD) Running: /home/abhay/Desktop/rcg-research/personal-work/ CHIMERA/bin/amber11/bin/atomtype -i ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff
Error while processing /home/abhay/Desktop/dockprep.py: Failure running ANTECHAMBER for residue NAD Check reply log for details
I am not sure what the problem is. $AMBERHOME and $DOCK_HOME are not defined, but that only seemed to cause problems before. Perhaps they need to be defined now? I would give you the reply log, but I don't know how to find it. I tried using:
$ ./chimera --start Reply_Log --nogui pdb:2h4f $DESKTOP/dockprep.py
I also tried reply_log, Reply_log, reply_Log, ReplyLog, replyLog, Replylog, and transposing --start and --nogui. None of those worked either. The program immediately returns:
Starting extension 'Reply_Log' failed (or whatever the pertinent permutation of "reply_log" happens to be.)
Assuming this can be fixed easily, I have one more question: this appears to only prepare the receptor for docking. What about prepping the ligand? Does that need its own new script?
Thank you so much for your help,
-Brad
On Wed, Feb 29, 2012 at 7:08 PM, Eric Pettersen <pett@cgl.ucsf.edu> wrote: This previous posting to the dock-fans list seems to be more directly pertinent:
http://mailman.docking.org/pipermail/dock-fans/2007-May/001043.html
--Eric
Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu
On Feb 29, 2012, at 2:47 PM, Trent E. Balius wrote:
Hi Brad,
I am cc'ing this to the chimera list.
I think that you should write a python script to run DOCK prep on the command line. See the following:
http://www.cgl.ucsf.edu/pipermail/chimera-dev/2011/000784.html
For other example scripts see the following:
http://www.cgl.ucsf.edu/pipermail/chimera-users/2009-February/003539.html
You should not have to specify the AMBERHOME path. This is done internally to chimera.
as an aside, It is unnecessary to run antichamber with sudo.
I hope this helps,
Trent E. Balius Graduate Student, Rizzo Group, Department of Applied Mathematics and Statistics, Stony Brook University. Office: Math Tower 3-129, Phone: (631) 632-8519 URL: http://www.ams.sunysb.edu/~tbalius/
-----Original Message----- From: Brad Ridder <clustro@gmail.com> To: dock-fans <dock-fans@docking.org> Sent: Wed, Feb 29, 2012 4:38 pm Subject: [Dock-fans] Help with antechamber
Hi Dockfans,
My name is Brad; I am a grad student in the dept. of chemical engineering at Purdue University.
We are experimenting with DOCK for various drug discovery work. At the moment, I am trying to do execute all of the "dock prep" commands through the Terminal, since it is not practical to do large volumes of Dock Prep by hand through the CHIMERA GUI.
Corresponding to what is in the DOCK tutorial, I am on "Receptor and Ligand Preparation." I got reduce to work, in order to add hydrogens.
Now, I am trying to get antechamber to work, in order to add the charges, but it is not working. Here is the command I am running:
sudo ./antechamber -i $DESKTOP/3GLR.pdb -fi pdb -o $DESKTOP/ 3GLRcharged.mol2 -fo mol2
Which returns the error:
Warning: $AMBERHOME and $DOCK_HOME enviornment strings are not set, use "mopac.sh" in the work directory
Cannot open CONNECT.TPL , exit The atom number exceeds the MAXATOM, reallocate memory
I looked around in the dock6 directory, and found a folder called "parameters/antechamber", which contains CONNECT.TPL. I figured this is what should be the $AMBERHOME directory. For DOCK_HOME, I figured it should be the dock6 folder.
Here is what I have in my .bash_profile file in my home folder.
export AMBERHOME='/home/.../DOCK6.5/dock6/parameters/antechamber' export DOCK_HOME='/home/.../DOCK6.5/dock6'
I also tried using the "amber11" folder that comes with CHIMERA as AMBERHOME, but to no effect.
I don't actually have AMBER installed on my computer, but since CHIMERA can add charges without actually requiring the purchase of AMBER, I do not think that is the problem.
I did not know what to do with "mopac.sh." I ran the script, but it says it needs input files.
What am I doing wrong that is preventing antechamber from executing correctly?
-- Bradley James Ridder Chakrabarti Group Graduate Student School of Chemical Engineering Purdue University
_______________________________________________ Dock-fans mailing list Dock-fans@docking.org http://mailman.docking.org/mailman/listinfo/dock-fans _______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
-- Bradley James Ridder Chakrabarti Group Graduate Student School of Chemical Engineering Purdue University
Hi, In addition to Eric's comments; 4) This post has a ligand prep script: http://mailman.docking.org/pipermail/dock-fans/2011-December/002591.html 5) Can you find and look at sqm.out ?? 6) Just as further evidence that NAD is tractable; see dock6/parameters/leap/parm/ndp.* (and again this is antechamber circa 2006). scott On Fri, Mar 16, 2012 at 02:37:54PM -0700, Eric Pettersen wrote:
Hi Brad, Well, a few things:
1) From your output I can tell that you are using an old version of Chimera. You should upgrade to the latest version (1.6.1) which includes a more recent version of antechamber with latest bug fixes.
2) I cannot get Chimera to fail on NAD (including old versions of Chimera). Does DockPrep work if you use it on 2h4f in regular, non-"nogui" mode? How about if you use it on 2gbp? Also, do you even want NAD present in the receptor when you attempt docking?
3) You couldn't possibly bring up the reply log in nogui mode since it creates a window. It's irrelevant anyway since the reply log output is the stuff you are already seeing on standard output (it only goes into the reply log in gui mode). For posterity, the syntax you would have used to start the reply log is: --start "Reply Log".
4) You would likely prep the ligand separately, yes.
I am taking chimera-users off the reply-to for this, since I doubt most subscribers will be interested in the minutiae of this problem.
--Eric
On Mar 16, 2012, at 12:35 PM, Brad Ridder wrote:
Hi Eric,
I tried the dockprep.py file you pointed to me a few emails ago. It seems like its exactly what I am looking for. The only problem is I get an error at the moment; I also have two other questions about it.
ep.py file you pointed to me a few emails ago. It seems like its exactly what I am looking for. The only problem is I get an error at the moment; I also have two other questions about it.
Here is the command I used:
./chimera --nogui pdb:2h4f $DESKTOP/dockprep.py
The program then returns a bunch of text on what its doing. When adding the charges to the ligands with the AM1-BCC method is when the error pops up. Here is the (slightly abridged) error message, plus a few lines back:
Running ANTECHAMBER for residue NAD Running ANTECHAMBER command: /home/abhay/Desktop/rcg-research/ personal-work/CHIMERA/bin/amber11/bin/antechamber -ek qm_theory='AM1', grms_tol=0.02, tight_p_conv=0, scfconv=1.d-10, -i / tmp/tmplP08co/ante.in.mol2 -fi mol2 -o /tmp/tmplP08co/ante.out.mol2 - fo mol2 -c bcc -nc -1 -j 5 -s 2
(NAD) Total number of electrons: 344; net charge: -1
(NAD) Running: /home/abhay/Desktop/rcg-research/personal-work/ CHIMERA/bin/amber11/bin/sqm -O -i sqm.in -o sqm.out
(NAD) Error: cannot run "/home/abhay/Desktop/rcg-research/personal- work/CHIMERA/bin/amber11/bin/sqm -O -i sqm.in -o sqm.out" of bcc() in charge.c properly, exit
(NAD) Running: /home/abhay/Desktop/rcg-research/personal-work/ CHIMERA/bin/amber11/bin/bondtype -j part -i ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac
(NAD) Running: /home/abhay/Desktop/rcg-research/personal-work/ CHIMERA/bin/amber11/bin/atomtype -i ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff
Error while processing /home/abhay/Desktop/dockprep.py: Failure running ANTECHAMBER for residue NAD Check reply log for details
I am not sure what the problem is. $AMBERHOME and $DOCK_HOME are not defined, but that only seemed to cause problems before. Perhaps they need to be defined now? I would give you the reply log, but I don't know how to find it. I tried using:
$ ./chimera --start Reply_Log --nogui pdb:2h4f $DESKTOP/dockprep.py
I also tried reply_log, Reply_log, reply_Log, ReplyLog, replyLog, Replylog, and transposing --start and --nogui. None of those worked either. The program immediately returns:
Starting extension 'Reply_Log' failed (or whatever the pertinent permutation of "reply_log" happens to be.)
Assuming this can be fixed easily, I have one more question: this appears to only prepare the receptor for docking. What about prepping the ligand? Does that need its own new script?
Thank you so much for your help,
-Brad
On Wed, Feb 29, 2012 at 7:08 PM, Eric Pettersen <pett@cgl.ucsf.edu> wrote: This previous posting to the dock-fans list seems to be more directly pertinent:
http://mailman.docking.org/pipermail/dock-fans/2007-May/001043.html
--Eric
Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu
On Feb 29, 2012, at 2:47 PM, Trent E. Balius wrote:
Hi Brad,
I am cc'ing this to the chimera list.
I think that you should write a python script to run DOCK prep on the command line. See the following:
http://www.cgl.ucsf.edu/pipermail/chimera-dev/2011/000784.html
For other example scripts see the following:
http://www.cgl.ucsf.edu/pipermail/chimera-users/2009-February/003539.html
You should not have to specify the AMBERHOME path. This is done internally to chimera.
as an aside, It is unnecessary to run antichamber with sudo.
I hope this helps,
Trent E. Balius Graduate Student, Rizzo Group, Department of Applied Mathematics and Statistics, Stony Brook University. Office: Math Tower 3-129, Phone: (631) 632-8519 URL: http://www.ams.sunysb.edu/~tbalius/
-----Original Message----- From: Brad Ridder <clustro@gmail.com> To: dock-fans <dock-fans@docking.org> Sent: Wed, Feb 29, 2012 4:38 pm Subject: [Dock-fans] Help with antechamber
Hi Dockfans,
My name is Brad; I am a grad student in the dept. of chemical engineering at Purdue University.
We are experimenting with DOCK for various drug discovery work. At the moment, I am trying to do execute all of the "dock prep" commands through the Terminal, since it is not practical to do large volumes of Dock Prep by hand through the CHIMERA GUI.
Corresponding to what is in the DOCK tutorial, I am on "Receptor and Ligand Preparation." I got reduce to work, in order to add hydrogens.
Now, I am trying to get antechamber to work, in order to add the charges, but it is not working. Here is the command I am running:
sudo ./antechamber -i $DESKTOP/3GLR.pdb -fi pdb -o $DESKTOP/ 3GLRcharged.mol2 -fo mol2
Which returns the error:
Warning: $AMBERHOME and $DOCK_HOME enviornment strings are not set, use "mopac.sh" in the work directory
Cannot open CONNECT.TPL , exit The atom number exceeds the MAXATOM, reallocate memory
I looked around in the dock6 directory, and found a folder called "parameters/antechamber", which contains CONNECT.TPL. I figured this is what should be the $AMBERHOME directory. For DOCK_HOME, I figured it should be the dock6 folder.
Here is what I have in my .bash_profile file in my home folder.
export AMBERHOME='/home/.../DOCK6.5/dock6/parameters/antechamber' export DOCK_HOME='/home/.../DOCK6.5/dock6'
I also tried using the "amber11" folder that comes with CHIMERA as AMBERHOME, but to no effect.
I don't actually have AMBER installed on my computer, but since CHIMERA can add charges without actually requiring the purchase of AMBER, I do not think that is the problem.
I did not know what to do with "mopac.sh." I ran the script, but it says it needs input files.
What am I doing wrong that is preventing antechamber from executing correctly?
Hi Scott and Eric, Okay, so I suppose the problem was not using the latest version of Chimera when running dockprep.py. I now correctly get "dp.mol2" written to the working directory. Now, I am just confused to where this puts me in the 4-step process. In the tutorial, this .mol2 file should correspond to everything up to and including step 1g in the tutorial. dp.mol2 has hydrogens in it, which need to be stripped away. I have a some new questions then: 1. I need to take dp.mol2, and make rec_noH.pdb from it. Is there a quick, easy way to do this with Chimera? e.g. open dp.mol2, strip the hydrogens, and save the results as a .pdb file? I see this commented-out code from ligprep.py could be useful: #runCommand('select H') #runCommand('delete sel') And also this "write" command: http://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/midas/write.html#opt... But how do I get python to use that "write" command? I don't understand why there is a "write" command here, but there is a totally separate python module "WriteMol2" just for writing .mol2 files. There is no "WritePDB." 2. I looked at the ligprep.py script, but I don't understand how to run it yet. First, where do you specify the input file? And what format does it have to be in? Also, there is some commented out code up top: # $HOME/chimera/1.2470/bin/chimera --nogui ligprep.py Is that just the command for running it from the terminal? It has no inputs specified, so the input file appears to be "start.sdf". Am I understanding this correctly? I am just confused because in the original message, the person wanted to loop over many files, but as this ligprep.py script is written, I don't see how any looping could be done since the input file is hard-coded to be "start.sdf". 3. In the case of 2H4F, I have more than one ligand. I want to keep the large peptide fixed (it has a long lysine pointing into the center of the enzyme), but NAD is what I want to dock. How would I tell Chimera/Python to choose NAD for ligand preparation? 4. The module "chimera" needs to be imported. However, I have three versions of Chimera on my computer: 1.5.3, 1.6, and 1.6.1. How will the Python import command know to go into the 1.6.1 directory to find the correct, up-to-date module files? Just adding the /chimera/share folder to the python path should work, right? 5. Is there a special procedure for deleting the other Chimera versions, or just trash them? All the best, and thank you so much for your help, -Brad On Fri, Mar 16, 2012 at 11:23 PM, Scott Brozell <sbrozell@rci.rutgers.edu>wrote:
Hi,
In addition to Eric's comments; 4) This post has a ligand prep script: http://mailman.docking.org/pipermail/dock-fans/2011-December/002591.html
5) Can you find and look at sqm.out ??
6) Just as further evidence that NAD is tractable; see dock6/parameters/leap/parm/ndp.* (and again this is antechamber circa 2006).
scott
On Fri, Mar 16, 2012 at 02:37:54PM -0700, Eric Pettersen wrote:
Hi Brad, Well, a few things:
1) From your output I can tell that you are using an old version of Chimera. You should upgrade to the latest version (1.6.1) which includes a more recent version of antechamber with latest bug fixes.
2) I cannot get Chimera to fail on NAD (including old versions of Chimera). Does DockPrep work if you use it on 2h4f in regular, non-"nogui" mode? How about if you use it on 2gbp? Also, do you even want NAD present in the receptor when you attempt docking?
3) You couldn't possibly bring up the reply log in nogui mode since it creates a window. It's irrelevant anyway since the reply log output is the stuff you are already seeing on standard output (it only goes into the reply log in gui mode). For posterity, the syntax you would have used to start the reply log is: --start "Reply Log".
4) You would likely prep the ligand separately, yes.
I am taking chimera-users off the reply-to for this, since I doubt most subscribers will be interested in the minutiae of this problem.
--Eric
On Mar 16, 2012, at 12:35 PM, Brad Ridder wrote:
Hi Eric,
I tried the dockprep.py file you pointed to me a few emails ago. It seems like its exactly what I am looking for. The only problem is I get an error at the moment; I also have two other questions about it.
ep.py file you pointed to me a few emails ago. It seems like its exactly what I am looking for. The only problem is I get an error at the moment; I also have two other questions about it.
Here is the command I used:
./chimera --nogui pdb:2h4f $DESKTOP/dockprep.py
The program then returns a bunch of text on what its doing. When adding the charges to the ligands with the AM1-BCC method is when the error pops up. Here is the (slightly abridged) error message, plus a few lines back:
Running ANTECHAMBER for residue NAD Running ANTECHAMBER command: /home/abhay/Desktop/rcg-research/ personal-work/CHIMERA/bin/amber11/bin/antechamber -ek qm_theory='AM1', grms_tol=0.02, tight_p_conv=0, scfconv=1.d-10, -i / tmp/tmplP08co/ante.in.mol2 -fi mol2 -o /tmp/tmplP08co/ante.out.mol2 - fo mol2 -c bcc -nc -1 -j 5 -s 2
(NAD) Total number of electrons: 344; net charge: -1
(NAD) Running: /home/abhay/Desktop/rcg-research/personal-work/ CHIMERA/bin/amber11/bin/sqm -O -i sqm.in -o sqm.out
(NAD) Error: cannot run "/home/abhay/Desktop/rcg-research/personal- work/CHIMERA/bin/amber11/bin/sqm -O -i sqm.in -o sqm.out" of bcc() in charge.c properly, exit
(NAD) Running: /home/abhay/Desktop/rcg-research/personal-work/ CHIMERA/bin/amber11/bin/bondtype -j part -i ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac
(NAD) Running: /home/abhay/Desktop/rcg-research/personal-work/ CHIMERA/bin/amber11/bin/atomtype -i ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff
Error while processing /home/abhay/Desktop/dockprep.py: Failure running ANTECHAMBER for residue NAD Check reply log for details
I am not sure what the problem is. $AMBERHOME and $DOCK_HOME are not defined, but that only seemed to cause problems before. Perhaps they need to be defined now? I would give you the reply log, but I don't know how to find it. I tried using:
$ ./chimera --start Reply_Log --nogui pdb:2h4f $DESKTOP/dockprep.py
I also tried reply_log, Reply_log, reply_Log, ReplyLog, replyLog, Replylog, and transposing --start and --nogui. None of those worked either. The program immediately returns:
Starting extension 'Reply_Log' failed (or whatever the pertinent permutation of "reply_log" happens to be.)
Assuming this can be fixed easily, I have one more question: this appears to only prepare the receptor for docking. What about prepping the ligand? Does that need its own new script?
Thank you so much for your help,
-Brad
On Wed, Feb 29, 2012 at 7:08 PM, Eric Pettersen <pett@cgl.ucsf.edu> wrote: This previous posting to the dock-fans list seems to be more directly pertinent:
http://mailman.docking.org/pipermail/dock-fans/2007-May/001043.html
--Eric
Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu
On Feb 29, 2012, at 2:47 PM, Trent E. Balius wrote:
Hi Brad,
I am cc'ing this to the chimera list.
I think that you should write a python script to run DOCK prep on the command line. See the following:
http://www.cgl.ucsf.edu/pipermail/chimera-dev/2011/000784.html
For other example scripts see the following:
http://www.cgl.ucsf.edu/pipermail/chimera-users/2009-February/003539.html
You should not have to specify the AMBERHOME path. This is done internally to chimera.
as an aside, It is unnecessary to run antichamber with sudo.
I hope this helps,
Trent E. Balius Graduate Student, Rizzo Group, Department of Applied Mathematics and Statistics, Stony Brook University. Office: Math Tower 3-129, Phone: (631) 632-8519 URL: http://www.ams.sunysb.edu/~tbalius/
-----Original Message----- From: Brad Ridder <clustro@gmail.com> To: dock-fans <dock-fans@docking.org> Sent: Wed, Feb 29, 2012 4:38 pm Subject: [Dock-fans] Help with antechamber
Hi Dockfans,
My name is Brad; I am a grad student in the dept. of chemical engineering at Purdue University.
We are experimenting with DOCK for various drug discovery work. At the moment, I am trying to do execute all of the "dock prep" commands through the Terminal, since it is not practical to do large volumes of Dock Prep by hand through the CHIMERA GUI.
Corresponding to what is in the DOCK tutorial, I am on "Receptor and Ligand Preparation." I got reduce to work, in order to add hydrogens.
Now, I am trying to get antechamber to work, in order to add the charges, but it is not working. Here is the command I am running:
sudo ./antechamber -i $DESKTOP/3GLR.pdb -fi pdb -o $DESKTOP/ 3GLRcharged.mol2 -fo mol2
Which returns the error:
Warning: $AMBERHOME and $DOCK_HOME enviornment strings are not set, use "mopac.sh" in the work directory
Cannot open CONNECT.TPL , exit The atom number exceeds the MAXATOM, reallocate memory
I looked around in the dock6 directory, and found a folder called "parameters/antechamber", which contains CONNECT.TPL. I figured this is what should be the $AMBERHOME directory. For DOCK_HOME, I figured it should be the dock6 folder.
Here is what I have in my .bash_profile file in my home folder.
export AMBERHOME='/home/.../DOCK6.5/dock6/parameters/antechamber' export DOCK_HOME='/home/.../DOCK6.5/dock6'
I also tried using the "amber11" folder that comes with CHIMERA as AMBERHOME, but to no effect.
I don't actually have AMBER installed on my computer, but since CHIMERA can add charges without actually requiring the purchase of AMBER, I do not think that is the problem.
I did not know what to do with "mopac.sh." I ran the script, but it says it needs input files.
What am I doing wrong that is preventing antechamber from executing correctly?
-- Bradley James Ridder Chakrabarti Group Graduate Student School of Chemical Engineering Purdue University
On Apr 9, 2012, at 4:41 PM, Brad Ridder wrote:
Hi Scott and Eric,
Hi Brad,
Okay, so I suppose the problem was not using the latest version of Chimera when running dockprep.py. I now correctly get "dp.mol2" written to the working directory. Now, I am just confused to where this puts me in the 4-step process. In the tutorial, this .mol2 file should correspond to everything up to and including step 1g in the tutorial.
I think that's correct.
dp.mol2 has hydrogens in it, which need to be stripped away.
I have a some new questions then:
1. I need to take dp.mol2, and make rec_noH.pdb from it. Is there a quick, easy way to do this with Chimera? e.g. open dp.mol2, strip the hydrogens, and save the results as a .pdb file? I see this commented-out code from ligprep.py could be useful:
#runCommand('select H') #runCommand('delete sel')
And also this "write" command:
http://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/midas/write.html#opt...
But how do I get python to use that "write" command? I don't understand why there is a "write" command here, but there is a totally separate python module "WriteMol2" just for writing .mol2 files. There is no "WritePDB."
You could just add some lines to dockprep.py script to also write out the PDB file, keeping in mind that the runCommand function can be used to run any Chimera command. So you would probably add lines like these: from chimera import runCommand runCommand('select H') runCommand('delete sel') runCommand('write 0 rec_noH.pdb') Alternatively you could write it as a separate script that opened the dp.mol2 file from the previous script if that was better for your workflow.
2. I looked at the ligprep.py script, but I don't understand how to run it yet. First, where do you specify the input file? And what format does it have to be in? Also, there is some commented out code up top:
# $HOME/chimera/1.2470/bin/chimera --nogui ligprep.py
Is that just the command for running it from the terminal? It has no inputs specified, so the input file appears to be "start.sdf". Am I understanding this correctly? I am just confused because in the original message, the person wanted to loop over many files, but as this ligprep.py script is written, I don't see how any looping could be done since the input file is hard-coded to be "start.sdf".
If you are going to use Scott's ligprep.py script, it looks like you would need to use it in a shell script that copies the input to start.sdf and then copies the output from start.mol2. In csh syntax, something like this: foreach sdf in (*.sdf) cp $sdf start.sdf chimera --nogui ligprep.py cp start.mol $sdf:r.mol2
3. In the case of 2H4F, I have more than one ligand. I want to keep the large peptide fixed (it has a long lysine pointing into the center of the enzyme), but NAD is what I want to dock. How would I tell Chimera/Python to choose NAD for ligand preparation?
Strip everything but NAD from the system to prep it as a ligand. Treat the peptide as part of the receptor, not as a ligand.
4. The module "chimera" needs to be imported. However, I have three versions of Chimera on my computer: 1.5.3, 1.6, and 1.6.1. How will the Python import command know to go into the 1.6.1 directory to find the correct, up-to-date module files? Just adding the /chimera/share folder to the python path should work, right?
You run a Chimera Python script with "chimera --nogui" not with the system Python. "chimera --nogui" will have the correct module paths.
5. Is there a special procedure for deleting the other Chimera versions, or just trash them?
On Windows there is a de-installer. On the Mac, just drag them to the Trash. --Eric
participants (4)
-
Brad Ridder -
Eric Pettersen -
Scott Brozell -
Trent E. Balius