GROMACS version:2018.1-1
GROMACS modification: Yes/No
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hello
i have done 3 to 4 simulation on gromacs and gives good results. but now i am trying to increase the the ns so its show error when I apply every force field. i have checked it on other than my protein and the error is same. however in my friend computer it worked very well.
going to rename charmm27.ff/aminoacids.r2b
Opening force field file /usr/share/gromacs/top/charmm27.ff/aminoacids.r2b
going to rename charmm27.ff/rna.r2b
Opening force field file /usr/share/gromacs/top/charmm27.ff/rna.r2b
Reading AF.pdb…
Read ‘SODIUM/POTASSIUM-TRANSPORTING ATPASE SUBUNIT BETA-1’, 2482 atoms
Analyzing pdb file
Splitting chemical chains based on TER records or chain id changing.
There are 1 chains and 0 blocks of water and 304 residues with 2482 atoms
chain #res #atoms
1 ‘A’ 304 2482
All occupancies are one
All occupancies are one
Opening force field file /usr/share/gromacs/top/charmm27.ff/atomtypes.atp
Reading residue database… (Charmm27)
Opening force field file /usr/share/gromacs/top/charmm27.ff/aminoacids.rtp
Opening force field file /usr/share/gromacs/top/charmm27.ff/dna.rtp
Opening force field file /usr/share/gromacs/top/charmm27.ff/lipids.rtp
Opening force field file /usr/share/gromacs/top/charmm27.ff/rna.rtp
Opening force field file /usr/share/gromacs/top/charmm27.ff/aminoacids.hdb
Opening force field file /usr/share/gromacs/top/charmm27.ff/dna.hdb
Opening force field file /usr/share/gromacs/top/charmm27.ff/lipids.hdb
Opening force field file /usr/share/gromacs/top/charmm27.ff/rna.hdb
Opening force field file /usr/share/gromacs/top/charmm27.ff/aminoacids.n.tdb
Opening force field file /usr/share/gromacs/top/charmm27.ff/dna.n.tdb
Opening force field file /usr/share/gromacs/top/charmm27.ff/rna.n.tdb
Opening force field file /usr/share/gromacs/top/charmm27.ff/aminoacids.c.tdb
Program: gmx pdb2gmx, version 2024-dev-20230329-26add465fa-dirty
Source file: src/gromacs/gmxpreprocess/ter_db.cpp (line 138)
Function: void read_atom(char*, bool, std::string*, t_atom*, PreprocessingAtomTypes*, int*)
Inconsistency in user input:
Atom type OH specified in terminal database has not been defined in the force
field
i have download the protein again and it shos the same error on every protein.