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

Eric Pettersen pett at cgl.ucsf.edu
Mon Feb 4 11:14:15 PST 2008


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 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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>
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