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"
<jalem...@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.pig...@bristol.ac.uk
University of Bristol, UK.
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