GROMACS version:2023
GROMACS modification: No
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I have made coarse-grained force field.
First, I just considered gly-gly interaction and wanted to simulate it. However, error like below occurred when executing gmx grompp:
ERROR 1 [file param.itp, line 15]:
Atomtype P5 not found
However, I defined atom type P5 in param.itp.
param.itp is below.
[ defaults ]
2 1
[ atomtypes ]
P5 72.0 0.0 A 0.0 0.0
[ nonbond_params ]
; i j func a b c
P5 P5 2 -15.0437661 3.48198326 -0.02315786
[ moleculetype ]
; molname nrexcl
GLY 1
[ atoms ]
; id at type res nr residu name at name cg nr charge
1 P5 1 GLY BAS 1 0
Line 15 where error occured is “P5 P5 2 -15.0437661 3.48198326 -0.02315786”
The first term, 2, in [ defaults ] is for setting the default potential as Buckingham potential.
below is topol.top file.
#ifdef POSRES_WATER
; Position restraint for each water oxygen
[ position_restraints ]
; i funct fcx fcy fcz
1 1 1000 1000 1000
#endif
; Include topology for ions
#include “atomtypes.atp”
#include “param.itp”
[ system ]
; Name
Generated by gmx solvate in water
[ molecules ]
; Compound #mols
GLY 22
How can I solve the problem?