[Dock-fans] [Chimera-users] cofactors in dock

Eric Pettersen pett at cgl.ucsf.edu
Thu May 17 13:45:41 PDT 2012


Yes, if you use the 1.6.1 release of Chimera, GTP is treated as a  
"standard" residue in that Chimera knows what the charges are for each  
atom without having to call antechamber to compute them (that  
computation typically fails with highly negatively charged molecules  
like GTP).

--Eric

                         Eric Pettersen
                         UCSF Computer Graphics Lab
                         http://www.cgl.ucsf.edu

On May 17, 2012, at 12:50 PM, Scott Brozell wrote:

> Hi,
>
> On Wed, May 16, 2012 at 03:22:11PM +0530, Mary Varughese wrote:
>> I have to include the cofactor GTP as part of my receptor protein  
>> and dock
>> with a ligand. But chimera is not allowing to prepare  
>> rec_charged.mol2 file
>> since it fails at finding amibcc charge method for GTP residue.  
>> Then i
>> separately prepared the mol2 file for GTP (using gtp.prep and  
>> gtp.frcmod)
>> and after performing dockprep on the receptor i opened the GTP.mol2  
>> file in
>> the same window and write the mol2 file. but again at grid  
>> generation it
>> fails "Reading in coordinates of receptor.
>> WARNING assign_vdw_labels: Atom valence violated for 1SA0.pdb  
>> (combined)
>> **** GTP 848 C8 13145.
>> Error reading in receptor."
>
> Which version of chimera are you using ?
> There was some recent activity for GTP but using Gasteiger charges:
> http://plato.cgl.ucsf.edu/pipermail/chimera-users/2011-October/006846.html
>
> Are you saying that you ran antechamber separately from chimera
> and got the am1bcc charges for gtp ?
>
> scott


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