Saumya wrote:
Hello all,
I am trying to simulate the DMPC Lipid Bilayer with water molecules. I
am using Charmm27 forcefield for that. I obtain the starting structure
from Charmm-GUI. The pdb file that I obtain has "DMPC" as the residue
name for the lipid molecules. I checked the "lipid.rtp" file in Charmm27
and it has DMPC in the list of lipids. But, when I generate the topology
using pdb2gmx, it says that it does not recognize the the DMPC residue.
Please copy and paste the exact error message.
Therefore, the resulting topology file does not include any information
about the lipids and only states the solvent information.
How can I generate a topology that will include the DMPC lipids too and
what residues name is recognized by Gromacs for the DMPC lipid?
Without seeing the error, it's hard to say. Also note that pdb2gmx is not
typically used for many-molecule systems like bilayers. You'll get a redundant
topology that is not wrong, but will be very cumbersome to use and understand.
The better approach is to:
1. Isolate a single DMPC lipid from your .pdb file
2. Run pdb2gmx on this single lipid
3. Modify the resulting .top into a .itp file (see
http://www.gromacs.org/Documentation/File_Formats/.itp_File)
4. Construct a simple topology, i.e.:
#include "charmm27.ff/forcefield.itp"
#include "dmpc.itp"
#include (water model you need)
[ system ]
whatever
[ molecules ]
(fill this in)
-Justin
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
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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