[Dock-fans] How to get the charged mol for the ligand

Eric Pettersen pett at cgl.ucsf.edu
Sun Feb 3 13:27:57 PST 2008


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 at 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 at 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 at 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 at cgl.ucsf.edu>
> Date: January 31, 2008 12:54:24 PM PST
> To: dock-fans at 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 at 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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