Ligand MD simulation

User discussions
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1

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:

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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
…

2

Sometimes you have to reorganize contents of itp files, but in this case I think it will be enough if you avoid repeating #include “gromos54a7_atb.ff/forcefield.itp”. You can only include the force field once (at the top), you are including it three times. You should include the water model itp file and the ions.itp file from the force field directory.

3

Oh I did it, thank you so much for your suggestion