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

cpsosa at comcast.net cpsosa at comcast.net
Sat Feb 2 17:19:27 PST 2008


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
> 
> 


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