[gmx-users] Adding ion to force field

Irem Altan irem.altan at duke.edu
Wed Oct 21 01:19:34 CEST 2015


I am trying to add an ion to amber99sb.ff. For this, I copied the amber99sb.ff folder to the folder I’m working in, and I also copied residuetypes.dat into the same directory. However, when I do pdb2gmx -f 1ytt_refine_001.pdb -ff amber99sb.ff -o box.gro -p topol.top, I get an error saying Could not find force field 'amber99sb.ff' in current directory, install tree or GMXDATA path.
I am using GROMACS 4.6.5. My working folder looks something like:

1ytt_refine_001.pdb  nvt.mdp                               residuetypes.dat           topol.top
amber99sb.ff         posre_Protein_chain_A.itp             topol_Protein_chain_A.itp  posre_Protein_chain_B.itp  topol_Protein_chain_B.itp

and the contents of amber99sb.ff  are:

aminoacids.arn    aminoacids.r2b  dna.arn  ffbonded.itp     gbsa.itp  rna.r2b   tip3p.itp    urea.itp
aminoacids.c.tdb  aminoacids.rtp  dna.hdb  ffnonbonded.itp  ions.itp  rna.rtp   tip4pew.itp  watermodels.dat
aminoacids.hdb    aminoacids.vsd  dna.r2b  forcefield.doc   rna.arn   spce.itp  tip4p.itp
aminoacids.n.tdb  atomtypes.atp   dna.rtp  forcefield.itp   rna.hdb   spc.itp   tip5p.itp

I only modified ffbonded.itp ions.itp atomtypes.atp  within the force field folder, and also residuetypes.dat in the working folder. What could be the problem?


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