[gmx-users] problem in simulation of DMPC lipid bilayer

nitu sharma sharmanitu35 at gmail.com
Wed Mar 25 08:39:15 CET 2009

Dear all,

                      I am using DMPC lipid bilayer from teleman sir
website  to insert my protein in this lipid bilayer .I have done this by
using command genbox. After that when I have run the command -
 pdb2gmx -f tap-in-dmpc.pdb -o tap-in-dmpc.gro -p tap-in-dmpc.top -i
tap-in-dmpc-itp -ff oplsaa

Error like this-

There are 0 hydrogen bonds
Warning: 'DMP' not found in residue topology database, trying to use 'DMSO'

Program pdb2gmx, VERSION 4.0.3
Source code file: pdb2gmx.c, line: 429

Fatal error:
Atom C1 in residue DMSO 1 not found in rtp entry with 10 atoms
             while sorting atoms
so please tell me how can I add DMP in residue topology database if anyone
has knowledge about this. And please if also u know about any site of lipid
bilayer from where i can download lipid bilayer then let me know.

thanks in advance

Nitu Sharma

School of life siences
Jawaherlal Nehru University
New Delhi ,India

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