[gmx-users] Re: Charmm36 FF and membrane

Thomas Piggot t.piggot at soton.ac.uk
Mon Nov 1 11:51:58 CET 2010


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:




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
> Tel: 022-2559 0300
> email: tusaratbarc at gmail.com <mailto:tusaratbarc at gmail.com>

Dr Thomas Piggot
University of Southampton, UK.

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