Ligand MD simulation

nhina
Fri, 08 Nov 2024 04:45:12 +0000
User discussions

GROMACS version: 2019.6
Hi guys,
I am performing a MD simulation for ligand only in the FEP calculations framework. The ligand molecules are parameterized by ATP website for gromos force field. Now, I get error about forcefield.itp when I run command: gmx grompp -f em.mdp -c lig.pdb -p top.top -o ion.tpr.
I think the problem is that I am missing [atomtypes] section in itp file. However, the *.itp of ligand is automatically generated by web server, so how can I fix this problem?
I will attach both my top.top and MOL_GMX.itp files. I hope someone can suggest me other option or how to fix this error. If you want me to send more information about em.mdp, please leave me a comment.
Thanks a lot in advance

My error:

forcefield…itp

#define _FF_GROMOS96
#define _FF_GROMOS54A7

[ defaults ]
; nbfunc comb-rule gen-pairs fudgeLJ fudgeQQ
1 1 no 1.0 1.0

#include “ffnonbonded.itp”
#include “ffbonded.itp”

My top.top

; Include forcefield parameters
#include “gromos54a7_atb.ff/forcefield.itp”
#include “MOL_GMX.itp”

; Include water topology
#include “gromos54a7_atb.ff/forcefield.itp”

#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 “gromos54a7_atb.ff/forcefield.itp”

[ system ]
; Name
Protein in water

[ molecules ]
; Compound #mols
G3R0 1

SOL 2157

My *.itp for ligand
[ moleculetype ]
; Name nrexcl
G3R0 3
[ atoms ]
; nr type resnr resid atom cgnr charge mass
1 CH3 1 G3R0 C14 1 0.091 15.0350
2 NTer 1 G3R0 N4 2 -0.256 14.0067
3 CH2 1 G3R0 C12 3 0.077 14.0270
4 CH2 1 G3R0 C11 4 0.207 14.0270
5 NOpt 1 G3R0 N3 5 -0.841 14.0067
6 CH2 1 G3R0 C15 6 0.195 14.0270
7 CH2 1 G3R0 C13 7 0.053 14.0270
8 SDmso 1 G3R0 S1 8 2.852 32.0600
9 OM 1 G3R0 O1 9 -0.917 15.9994
10 OM 1 G3R0 O2 10 -0.917 15.9994
11 CAro 1 G3R0 C8 11 -0.799 12.0110
12 CAro 1 G3R0 C7 12 -0.022 12.0110
13 HC 1 G3R0 H24 13 0.162 1.0080
14 CAro 1 G3R0 C6 14 -0.144 12.0110
15 HC 1 G3R0 H25 15 0.148 1.0080
16 CAro 1 G3R0 C5 16 0.018 12.0110
17 CAro 1 G3R0 C10 17 -0.144 12.0110
18 HC 1 G3R0 H26 18 0.148 1.0080
19 CAro 1 G3R0 C9 19 -0.022 12.0110
20 HC 1 G3R0 H27 20 0.162 1.0080
21 CAro 1 G3R0 C1 21 -0.113 12.0110
22 NOpt 1 G3R0 N1 22 -0.075 14.0067
23 CAro 1 G3R0 C2 23 -0.242 12.0110
24 CAro 1 G3R0 C4 24 0.185 12.0110
25 NOpt 1 G3R0 N2 25 -0.166 14.0067
26 CAro 1 G3R0 C3 26 0.003 12.0110
27 HC 1 G3R0 H28 27 0.196 1.0080
28 NPri 1 G3R0 N8 28 -0.324 14.0067
29 HS14 1 G3R0 H2 29 0.257 1.0080
30 HS14 1 G3R0 H3 30 0.257 1.0080
…

3 posts - 2 participants