[gmx-users] grompp error for alamethicin

[pragya chohan]

hi ... when i run grompp i get an error " No such moleculetype Protein " ... i included itp for ACE and AIB after generating them from PRODRG2 server... my top file is :

; Include forcefield parameters
#include "ffG43a1.itp"

; Include chain topologies
#include "ace.itp"
#include "aib.itp"

; Include water topology
#include "spce.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             1

The command i m using is :

grompp -f 7eq_w.mdp -c ala.gro -p aquapo_grom.top -o alam.tpr

ala.gro is generated using editconf.
The .mdp file is

integrator           = md
define               = -DPOSRES -DFLEX_SPC
dt                   = 0.002
nsteps               = 25000
nstxout              = 500
ns_type              = grid
pbc                  = xyz
constraints          = hbonds
constraints_algorithm= shake
coulombtype          = PME
vdwtype              = cut-off
rcoloumb             = 1.4

Tcoupl               = berendsen
pcoupl               = berendsen
tau_t                = 0.1       0.1
tc_grps              = POPC      SOL
ref_t                = 300       300
ref_p                = 1.0
pcoupltype           = isotropic
compressibility      = 4.5e-5
gen_temp             = 300

Pls reply as soon as possible

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