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

[Mark Abraham]

nitu sharma wrote:
> 
> 
> 
> 
> 
> 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.

You may find some helpful information 
http://wiki.gromacs.org/index.php/Membrane_Simulations and 
http://wiki.gromacs.org/index.php/Errors#Residue_.27XXX.27_not_found_in_residue_topology_database

Mark