[gmx-users] protein membrane simulation

[maite lopez]

Hi all:

I´m working on membrane peptides simulation under lipid (POPC, from
Peter Tieleman group site). I downloaded the popc.pdb and lipid.itp
file from this site and i want to use the ffG53a5 force field. Some
days ago suggest to me i should to do something like this :

http://www.gromacs.org/pipermail/gmx-users/2006-September/023639.html
http://www.gromacs.org/pipermail/gmx-users/2006-September/023640.html

These are the steps i followed:

1. Added [atomtypes] from lipid.itp to ffG53a5nb.itp and to ffG53a5.atp

2. Added [pairtypes] from lipid.itp to  ffG53a5nb.itp and  removed any
with reference to HW as it will be zero regardless.

3. Added [dihedraltypes] from lipid.itp to ffG53a5bon.itp.

My popc128.top file is:

; Include forcefield parameters
#include \"ffG53a5.itp\"

; Include water topology
#include \"spc.itp\"

#ifdef POSRES_WATER
; Position restraint for each water oxygen
[ position_restraints ]
;  i funct       fcx        fcy        fcz
   1    1       1000       1000       1000
#endif

[ system ]
; name
POPC128 + 2460 water

[ molecules ]
; name	number
POP     128
SOL     2460

But when i run grompp it gives :
Fatal error:
No such moleculetype POP

Could you help me?

another question:
Have somebody a script for deleting the  water molecules between the
monolayers (this molecules are added with genbox command).

All comments are very appreciated.
thanks
Maite