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
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-- Bradley James Ridder Chakrabarti Group Graduate Student School of Chemical Engineering Purdue University