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

[TJ Piggot]

I agree with Justin that the way to do this is by adding a new entry to the 
.rtp file. The only point I would make is that as you seem to be missing 
the gamma phosphate and its oxygens would it not make more sense to start 
from an ADP topology? Also you should ask (or have asked) yourself why 
these atoms are missing in your start structure and do they need to be 
added back or are they missing for a purpose.

Tom

--On Thursday, May 07, 2009 06:59:21 -0400 "Justin A. Lemkul" 
<jalemkul at vt.edu> wrote:

>
>
> 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
>>
>
> --
> ========================================
>
> 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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----------------------
TJ Piggot
t.piggot at bristol.ac.uk
University of Bristol, UK.