Re: [Chimera-users] [Dock-fans] How to get the charged mol for the ligand
Hi Carlos, There are basically three things you can do: 1) Download the latest daily build and try that. I have been working hard on atom typing for ring systems recently (and am still working on it) and there's a pretty good chance that it will type (and therefore protonate) the phenyl oxygen correctly now. You get a daily build by going to the Chimera home page (www.cgl.ucsf.edu/ chimera) and following the "Daily Builds" link. 2) Directly edit the structure (after adding hydrogens but before adding charges). Control-double-click the oxygen and select "Modify Atom" from the pop-up menu. In the resulting dialog change the element type to O, the geometry to tetrahedral, and the number of bonds to 2. You should also probably change the atom name field to be the same as what the atom's name is. Then click the Change button and the hydrogen will be added. 3) Before doing any processing, change the bond length. Control double-click on the C-O bond and choose "Set Bond Length" from the pop-up menu. Type in a bond length appropriate for a C-O single bond and then run the rest of your processing. --Eric Eric Pettersen UCSF Computer Graphics Lab On Feb 2, 2008, at 5:19 PM, cpsosa@comcast.net wrote:
Hello,
We have the opposite problem, our PDB has one oxygen that is part of a phenyl group and after using addH in Chimera, hydrogen does not get added to that oxygen. Is there a way to add hydrogen to a single atom? using Chimera. For Chimera to add a hydrogen to that O... perhaps making the C-O bond larger.
Any suggestions?
Thanks,
-- Carlos P. Sosa
-------------- Original message ---------------------- From: Eric Pettersen <pett@cgl.ucsf.edu>
I assume this is IMZ from 1rv1? Chimera is adding a proton to the N3 nitrogen that it shouldn't. After adding hydrogens and before saying OK to the charge calculation, type this command to Chimera's command line to delete the extra hydrogen:
del :IMZ@h3
--Eric
Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu
I could not get the charges for my molecule (ligand in x-crystal structure). how to do that? I am getting the following error message. I am using chimera to do these funtions.
Running ANTECHAMBER command: C:\Program Files\Chimera\bin \antechamber\exe\antechamber -i c:\docume~1\thomas\locals~1\temp \tmpkzw4il\ante.in.mol2 -fi mol2 -o c:\docume~1\thomas\locals~1\temp \tmpkzw4il\ante.out.mol2 -fo mol2 -c bcc -nc 1 -j 5 -s 2 (IMZ) (IMZ) Running: "C:\Program Files\Chimera\bin\antechamber"\exe \bondtype -i ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC - f ac -j part (IMZ) (IMZ) Running: "C:\Program Files\Chimera\bin\antechamber"\exe \atomtype -i ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff (IMZ) Total number of electrons: 351; net charge: 1 (IMZ) INFO: Number of electrons is odd: 351 (IMZ) Please check the total charge (-nc flag) and spin multiplicity (-m flag) Failure running ANTECHAMBER for residue IMZ
Thomas
From: Eric Pettersen <pett@cgl.ucsf.edu> Date: January 31, 2008 12:54:24 PM PST To: dock-fans@docking.org Subject: Re: [Dock-fans] How to get the charged mol for the ligand
I assume this is IMZ from 1rv1? Chimera is adding a proton to the N3 nitrogen that it shouldn't. After adding hydrogens and before saying OK to the charge calculation, type this command to Chimera's command line to delete the extra hydrogen:
del :IMZ@h3
--Eric
Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu
I could not get the charges for my molecule (ligand in x-crystal structure). how to do that? I am getting the following error message. I am using chimera to do these funtions.
Running ANTECHAMBER command: C:\Program Files\Chimera\bin \antechamber\exe\antechamber -i c:\docume~1\thomas\locals~1\temp \tmpkzw4il\ante.in.mol2 -fi mol2 -o c:\docume~1\thomas\locals~1 \temp\tmpkzw4il\ante.out.mol2 -fo mol2 -c bcc -nc 1 -j 5 -s 2 (IMZ) (IMZ) Running: "C:\Program Files\Chimera\bin\antechamber"\exe \bondtype -i ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac -j part (IMZ) (IMZ) Running: "C:\Program Files\Chimera\bin\antechamber"\exe \atomtype -i ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff (IMZ) Total number of electrons: 351; net charge: 1 (IMZ) INFO: Number of electrons is odd: 351 (IMZ) Please check the total charge (-nc flag) and spin multiplicity (-m flag) Failure running ANTECHAMBER for residue IMZ
Thomas
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I forgot, there's actually a fourth thing you can do: change the atom type directly. Select the oxygen atom and open the command line (Favorites->Command Line) and type: setattr a idatmType O3 sel which will set the selected atom's "idatmType" attribute to sp3 oxygen ("O3"). Do this before hydrogens are added. --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu On Feb 3, 2008, at 1:27 PM, Eric Pettersen wrote:
Hi Carlos, There are basically three things you can do:
1) Download the latest daily build and try that. I have been working hard on atom typing for ring systems recently (and am still working on it) and there's a pretty good chance that it will type (and therefore protonate) the phenyl oxygen correctly now. You get a daily build by going to the Chimera home page (www.cgl.ucsf.edu/chimera) and following the "Daily Builds" link.
2) Directly edit the structure (after adding hydrogens but before adding charges). Control-double-click the oxygen and select "Modify Atom" from the pop-up menu. In the resulting dialog change the element type to O, the geometry to tetrahedral, and the number of bonds to 2. You should also probably change the atom name field to be the same as what the atom's name is. Then click the Change button and the hydrogen will be added.
3) Before doing any processing, change the bond length. Control double-click on the C-O bond and choose "Set Bond Length" from the pop-up menu. Type in a bond length appropriate for a C-O single bond and then run the rest of your processing.
--Eric
Eric Pettersen UCSF Computer Graphics Lab
On Feb 2, 2008, at 5:19 PM, cpsosa@comcast.net wrote:
Hello,
We have the opposite problem, our PDB has one oxygen that is part of a phenyl group and after using addH in Chimera, hydrogen does not get added to that oxygen. Is there a way to add hydrogen to a single atom? using Chimera. For Chimera to add a hydrogen to that O... perhaps making the C-O bond larger.
Any suggestions?
Thanks,
-- Carlos P. Sosa
-------------- Original message ---------------------- From: Eric Pettersen <pett@cgl.ucsf.edu>
I assume this is IMZ from 1rv1? Chimera is adding a proton to the N3 nitrogen that it shouldn't. After adding hydrogens and before saying OK to the charge calculation, type this command to Chimera's command line to delete the extra hydrogen:
del :IMZ@h3
--Eric
Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu
I could not get the charges for my molecule (ligand in x-crystal structure). how to do that? I am getting the following error message. I am using chimera to do these funtions.
Running ANTECHAMBER command: C:\Program Files\Chimera\bin \antechamber\exe\antechamber -i c:\docume~1\thomas\locals~1\temp \tmpkzw4il\ante.in.mol2 -fi mol2 -o c:\docume~1\thomas\locals~1 \temp \tmpkzw4il\ante.out.mol2 -fo mol2 -c bcc -nc 1 -j 5 -s 2 (IMZ) (IMZ) Running: "C:\Program Files\Chimera\bin\antechamber"\exe \bondtype -i ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC - f ac -j part (IMZ) (IMZ) Running: "C:\Program Files\Chimera\bin\antechamber"\exe \atomtype -i ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff (IMZ) Total number of electrons: 351; net charge: 1 (IMZ) INFO: Number of electrons is odd: 351 (IMZ) Please check the total charge (-nc flag) and spin multiplicity (-m flag) Failure running ANTECHAMBER for residue IMZ
Thomas
From: Eric Pettersen <pett@cgl.ucsf.edu> Date: January 31, 2008 12:54:24 PM PST To: dock-fans@docking.org Subject: Re: [Dock-fans] How to get the charged mol for the ligand
I assume this is IMZ from 1rv1? Chimera is adding a proton to the N3 nitrogen that it shouldn't. After adding hydrogens and before saying OK to the charge calculation, type this command to Chimera's command line to delete the extra hydrogen:
del :IMZ@h3
--Eric
Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu
I could not get the charges for my molecule (ligand in x-crystal structure). how to do that? I am getting the following error message. I am using chimera to do these funtions.
Running ANTECHAMBER command: C:\Program Files\Chimera\bin \antechamber\exe\antechamber -i c:\docume~1\thomas\locals~1\temp \tmpkzw4il\ante.in.mol2 -fi mol2 -o c:\docume~1\thomas\locals~1 \temp\tmpkzw4il\ante.out.mol2 -fo mol2 -c bcc -nc 1 -j 5 -s 2 (IMZ) (IMZ) Running: "C:\Program Files\Chimera\bin\antechamber"\exe \bondtype -i ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac -j part (IMZ) (IMZ) Running: "C:\Program Files\Chimera\bin\antechamber"\exe \atomtype -i ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff (IMZ) Total number of electrons: 351; net charge: 1 (IMZ) INFO: Number of electrons is odd: 351 (IMZ) Please check the total charge (-nc flag) and spin multiplicity (-m flag) Failure running ANTECHAMBER for residue IMZ
Thomas
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Eric Pettersen