GROMACS version: 2019
GROMACS modification: Yes/No
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Hi guys,
I have a question related to ligand parameterization. I am working on protein-ligand complex simulation using gromacs version 2019.6. My protein is KLVFF which is a small sequence of amyloid. I used GROMOS96 54A7 to parameterize for protein. I am trying to parameterize for ligand following web tools ATB.
However, when i run command “gmx grompp -f em.mdp -maxwarn 2 -c rec_1.pdb -p top.top -o ion.tpr” to add ion, then it appears an error “Atomtype CAro not found”. I don’t know why gromos54a7 can not read MOL_GMX.itp file created by ATB. Can you have any others option to parameterize ligand use other gromos96 force field? I hope some one can suggest me other option or how to fix this error.
My top.top
; Created by:
; :-) GROMACS - gmx pdb2gmx, VERSION 2019.6 (-:
;
; Executable: /opt/gromacs/2019/bin/gmx
; Data prefix: /opt/gromacs/2019
; Command line:
; gmx pdb2gmx -f KLVFF.pdb -ignh -p top.top -o rec.pdb -ter
; Force field was read from the standard GROMACS share directory.
;
; Include forcefield parameters #include “gromos54a7.ff/forcefield.itp” #include “MOL_GMX.itp”
; Include chain topologies #include “top_Protein_chain_A.itp” #include “top_Protein_chain_A2.itp”
; Include water topology #include “gromos54a7.ff/spc.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.ff/ions.itp”
Probably you need to write line #include “MOL_GMX.itp” after protein topologies. Because NGOC appears after protein in [molecules] section and likely in .gro file.
Actually, i think it is not a key of this problem, because at the first time i write
Include chain topologies #include “top_Protein_chain_A.itp” #include “top_Protein_chain_A2.itp” #include “MOL_GMX.itp”
but it still has the same error, so i think this error relating to force field.
MOL_GMX.itp seems to use atomtypes that are not specified in the force field. Do you get any other (itp) files from ATB? Do they contain an [ atomtypes ] section?
ATB replied me with two itp files. One of them contains all atom and another contains united atom. However, in both of them don’t contain [ atomtypes ] section. They only contain sections as [ atoms ], [ bonds ], [ pairs ], [ angles ], [ dihedrals ], [ dihedrals ], [ exclusions ]. Does the lack of atomtypes affect reading the itp file?
The atomtype CAro is not defined in the standard Gromos force field (at least not the one that is shipped with GROMACS). So you will need to find the correct atom type data for that (and possibly other) atom type.