Hi,
This is more of a GROMACS problem than a specific problem related to
this lipid conversion so it is best to keep these questions on the
GROMACS mailing list (I have copied my reply there).
The warning is fairly explanatory, your input POPE structure (for POPE
315) is missing this hydrogen. This means that whatever you did in VMD
to generate the structure did not add this hydrogen. You should have
been able to solve this by adding the appropriate lines into the .hdb
(which is left empty as the user is expected to provide an all-atom
lipid input structure, the same as in the CHARMM27 forcefield in
GROMACS). I cannot tell why this has not worked without you providing
more details of what you did.
However, rather than trying to either fix what you did in VMD or add
entries into the .hdb, the easiest solution is to your problem is to
just use an available CHARMM36 bilayer as input for pdb2gmx:
http://terpconnect.umd.edu/~jbklauda/research/download.html
Cheers
Tom
tusar ban wrote:
Dear Prof.Piggot,
I am trying to equilibrate POPE membrane (generated though VMD) using
Gromacs 4.5.1 and Charmm36 FF. I have downloaded "charmm36.ff.tgz
<http://www.gromacs.org/@api/deki/files/127/=charmm36.ff.tgz>" from
http://www.gromacs.org/Downloads/User_contributions/Force_fields. When I
do pdb2gmx, I get several warnings, all about H-atoms. One such typical
warning is
"WARNING: atom H6Y is missing in residue POPE 315 in the pdb file
You might need to add atom H6Y to the hydrogen database of
building block POPE
in the file lipids.hdb"
I opened the "lipids.hdb" file and found that is empty. What could be
the reason for this. Is it intentionally kept empty?
When I manually prepare the "lipids.hdb" (following the Gromacs Manual),
I could successfully pdb2gmx, energy minimize the POPE membrane.
However, I could not equilibrate the minimized structure. During
equilibration, mdrun works up to few thousand steps and then started
complaining about LJ 1-4 interactions and it crashes. I do not know
where I went wrong. Please enlighten me.
Best regards.
--
Dr. Tusar Bandyopadhyay
Theoretical Chemistry Section,
Chemistry Group
BARC, Trombay
Mumbai 400 085
INDIA
Tel: 022-2559 0300
email: [email protected] <mailto:[email protected]>
--
Dr Thomas Piggot
University of Southampton, UK.
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