[gmx-users] Fatal error: Atom CG is used in the topology database...

[Justin A. Lemkul]

Andy Somogyi wrote:
> Any suggestions for programmatically repairing the pdb, i.e. Guessing the missing residue atoms and adding them at the appropriate coordinates? 
> 
> I tried vmd's autopsf, which works, but evidently vmd's implementation of charm27 is different than Gromac's, it adds atom types not present in Gromac's charm27. 
> 
> I looked into whatif, but unfortunately it's not free OSS.
> 
> Wonder if I could use vmd's autopsf, and then write something that changes the atom types??
> 
> Any ideas?
> 

My favorite tool for simple sidechain rebuilding:

http://spdbv.vital-it.ch/

It offers a rotamer library and the naming conforms to the normal standard so 
there are no issues when using the fixed files as input into pdb2gmx.

-Justin

> Thanks
> 
> On Mar 23, 2012, at 5:39 PM, "Justin A. Lemkul" <jalemkul at vt.edu> wrote:
> 
>>
>> Andy Somogyi wrote:
>>> Hi All,
>>> I'm trying to generate topology for a PDB from viperdb, PDB ID 1DZL, http://viperdb.scripps.edu/info_page.php?VDB=1dzl
>>> using pdb2gmx -f 1dzl_full.pdb -o test.pdb -p test.top
>>> I've tried CHARMM27 and AMBER03 FFs, water none and I get the result:
>>> Fatal error:
>>> Atom CG is used in the topology database, but an atom of that
>>> name was not found in residue number 1.
>>> I have not have much luck finding this error in any mailing list.
>> I've never seen that error before, but it sounds like there is an atom named 'CG' in the .rtp entry but not in the coordinate file.  Either the atom is named differently or it is missing.
>>
>>> If the PDB does have missing atoms, can pdb2gmx guess missing atoms like VMD's psf gen?
>> No.  The contents of the input coordinate file must match what is expected by the .rtp file.  If you have missing atoms, they must be modeled in using external software.
>>
>> -Justin
>>
>> -- 
>> ========================================
>>
>> Justin A. Lemkul
>> Ph.D. Candidate
>> ICTAS Doctoral Scholar
>> MILES-IGERT Trainee
>> Department of Biochemistry
>> Virginia Tech
>> Blacksburg, VA
>> jalemkul[at]vt.edu | (540) 231-9080
>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>>
>> ========================================
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-- 
========================================

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

========================================