[gmx-users] Membrane Peptide+ DPPC+ Water simulation

[pandey at bioinfo.ernet.in]

Hi gmx users

 I am trying to simulate peptide+dppc+water system. I have used ffG43a2x
force field
 while pdb2gmx, then editconf and genbox with dppc_npat.pdb (downloaded
from P. Tieleman
 site.
 I am using Gromacs 3.2.1 on i386.

 I am facing problem while grompp run with energy minimization. I am using
default em.mdp
 provided on gromacs tutor with -DFLEX_SPC on and steep integrator.

I have tried following two options:
1)
Section of Topolgy file:
------------option 1---------------------
; Include forcefield parameters
#include "ffG43a2x.itp"
#include "dppc.itp"
[ moleculetype ]
; Name            nrexcl
Protein_A           3

[ atoms ]
[.......]

[......]

; Include Position restraint file
#ifdef POSRES
#include "posre.itp"
#endif

; 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

; Include generic topology for ions
#include "ions.itp"

[ system ]
; Name
Protein in water

[ molecules ]
; Compound        #mols
Protein_A           1
SOL              1319

---------error while grompp---------------
Back Off! I just backed up mdout.mdp to ./#mdout.mdp.5#
checking input for internal consistency...
calling /lib/cpp...
processing topology...
Generated 144 of the 1176 non-bonded parameter combinations
Cleaning up temporary file gromppoPmsqr
Fatal error: Atomtype 'LC3' not found!
-----------------end--------------------
2)Section of Topolgy file:

----------------option 2----------------
; Include forcefield parameters
#include "ffgmx.itp" ;;;;downloaded from gromacs site;;;
#include "dppc.itp" ;;;downloaded from Tieleman site
[ moleculetype ]
; Name            nrexcl
Protein_A           3
[atoms]
[.....]
[.....]
; Include Position restraint file
#ifdef POSRES
#include "posre.itp"
#endif

; 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

; Include generic topology for ions
#include "ions.itp"

[ system ]
; Name
Protein in water

[ molecules ]
; Compound        #mols
Protein_A           1
SOL              1319
---------error while grompp--------
Back Off! I just backed up mdout.mdp to ./#mdout.mdp.6#
checking input for internal consistency...
calling /lib/cpp...
processing topology...
Generated 1174 of the 2016 non-bonded parameter combinations
Cleaning up temporary file gromppYSCj7n
Fatal error: Atomtype 'HC' not found!
-----------end------------------------

I do not have any idea how to circumvent this problem.
Any help will be highly appreciated.