[gmx-users] atomtype c3 not found

[Monoj Mon Kalita]

Dear users

I am trying to simulate a ligand and protein in POPC. I have calculated the
ligand paramteres using the generalized amber force field (GAFF)  and now I
am trying to simulate the ligand-protein system with amber99sb-ildn ff.  I
have added the lines in the topology file like this


; Include forcefield parameters and compound atomtypes
#include "amber99sb-ildn.ff/forcefield.itp"
#include "ligand-non-bonded.itp"

; Include chain topologies
#include "topol_Protein.itp"

; Include water topology
#include "amber99sb-ildn.ff/spc.itp"
;Include ion parameters
#include "amber99sb-ildn.ff/ions.itp"

;Include compoud
#include "ligand.itp"

[ system ]
; Name
protein

[ molecules ]
Protein
SOL
MOL

But the grompp is not reading the ligand parameters. It is showing the
error 'atomtype c3 not found'.

These are the atomtypes in my ligand file from GAFF

 c3       c3          0.00000  0.00000   A     3.39967e-01   4.57730e-01 ;
1.91  0.1094
 n3       n3          0.00000  0.00000   A     3.25000e-01   7.11280e-01 ;
1.82  0.1700
 hc       hc          0.00000  0.00000   A     2.64953e-01   6.56888e-02 ;
1.49  0.0157
 hn       hn          0.00000  0.00000   A     1.06908e-01   6.56888e-02 ;
0.60  0.0157

which are already in the ligand-non-bonded.itp file.

Can anybody suggest me, how to solve this issue. I have seen this issue in
the archive, but didn't find much information in it.

http://comments.gmane.org/gmane.science.biology.gromacs.user/41031


with regards

Mon