[gmx-users] protein membrane simulation

maite lopez lopezmai at gmail.com
Wed Apr 4 21:39:57 CEST 2007

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 :


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\"

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

[ 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.

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