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.pig...@soton.ac.uk
<mailto:t.pig...@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: tusaratb...@gmail.com <mailto:tusaratb...@gmail.com>
<mailto:tusaratb...@gmail.com <mailto:tusaratb...@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: tusaratb...@gmail.com <mailto:tusaratb...@gmail.com>
--
Dr Thomas Piggot
University of Southampton, UK.
--
gmx-users mailing list gmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
