[gmx-users] lipid bilayer

[Pedro Alexandre de Araujo Gomes Lapido Loureiro]

> Hi
> I want to simulate a lipid bilayer, POPC. When I run pdb2gmx I receieve 
> the following error:
> residue "PALM" not found in residue topology database.
> I put lipid.itp and popc.itp in the folder where the force field's files are.
> 
> >From what I saw residues are defined in .rtp files. Should I modify this 
> file?
> 
> Regards,
> Tivadar, Orban 

Hello,

in fact, you have no need to run pdb2gmx or to modify the ff*.rtp files, as long
as you already have popc.itp.
All you have to do is to create a "short" topology file (popc.top, for instance)
such as:

#include "ffgmx.itp",(if you wish to use this forcefield !!)
#include "popc.itp"

#ifdef FLEX_SPC
#include "flexspc.itp"
#else
#include "spc.itp"
#endif

[ system ]
; name
xxxxxxx

[ molecules ]
; name  number
POPC     xx
SOL      xx
 
But do read the manual pages 96-98 (version 3.0).

Cheers,
Pedro.

--
Pedro Alexandre Lapido Loureiro
Laboratório de Física Biológica
Instituto de Biofísica
UFRJ
Brasil