[gmx-users] Re: Charmm36 FF and membrane

[Thomas Piggot]

As I said please keep all correspondence on the GROMACS mailing list for 
general GROMACS problems.

You can use genconf to increase the size of the membrane.

Cheers

Tom

tusar ban wrote:
> Thanks for your reply. The link that you have suggested contains the 
> POPE structure. However that is too small (by XY dimension) for my 
> purpose. I am still trying with Charmm36 FF.
> Regards
> 
> On Mon, Nov 1, 2010 at 4:21 PM, Thomas Piggot <t.piggot at soton.ac.uk 
> <mailto:t.piggot at soton.ac.uk>> wrote:
> 
>     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
>     <http://terpconnect.umd.edu/%7Ejbklauda/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: tusaratbarc at gmail.com <mailto:tusaratbarc at gmail.com>
>         <mailto:tusaratbarc at gmail.com <mailto:tusaratbarc at gmail.com>>
> 
> 
>     -- 
>     Dr Thomas Piggot
>     University of Southampton, UK.
> 
> 
> 
> 
> -- 
> Dr. Tusar Bandyopadhyay
> Theoretical Chemistry Section,
> Chemistry Group
> BARC, Trombay
> Mumbai 400 085
> INDIA
> Tel: 022-2559 0300
> email: tusaratbarc at gmail.com <mailto:tusaratbarc at gmail.com>
> 

-- 
Dr Thomas Piggot
University of Southampton, UK.