[gmx-users] atom name O3PB not found in residue ATP 340 while generating exclusions when running pdb2gmx

[Justin A. Lemkul]

Una Bjarnadottir wrote:
> Dear all,
> 
> I'm running a simulation of a structure which has part of ATP bound to 
> it so I'm using the -missing command when running pdb2gmx
> 
> pdb2gmx runs and lists the missing atoms and than it gives a fatal error 
> about missing atom name!
> 
> WARNING: atom O3PB is missing in residue ATP 340 in the pdb file
> WARNING: atom APG is missing in residue ATP 340 in the pdb file
> WARNING: atom O1PG is missing in residue ATP 340 in the pdb file
> WARNING: atom O2PG is missing in residue ATP 340 in the pdb file
> WARNING: atom O3PG is missing in residue ATP 340 in the pdb file
> WARNING: atom H3PG is missing in residue ATP 340 in the pdb file
>         You might need to add atom H3PG to the hydrogen database of 
> residue ATP
>         in the file ff???.hdb (see the manual)
> 
> There were 17 missing atoms in molecule Protein_A
> Number of bonds was 3730, now 3725
> Generating angles, dihedrals and pairs...
> Fatal error: atom name O3PB not found in residue ATP 340 while 
> generating exclusions
> 

The [ exclusions ] are pre-defined in the force field .rtp file.  The easiest 
way I can see to get around this is to make a local copy of the .rtp file, make 
a new entry for your molecule based on the ATP entry (deleting out whatever 
atoms are not present) and trying again, using a new name for this partial ATP, 
in both the .rtp and .pdb files.

The -missing option, as described by pdb2gmx is "dangerous" for this reason.

-Justin
> How can I resolve this  first not done by -missing command?
> 
> Cheers, Una
> 

-- 
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
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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