GROMACS version: 2023.5
GROMACS modification: Yes
I am trying to generate a topology file for a tripeptide molecule (Glutathione).
As you know, it has Glycine, Cysteine, and Glutamic Acid.
I built the pdb file by considering protonation for three groups
1.) COO- (Glycine)
2.) COO- (Gluta)
3.) NH3+ (Gluta)
Also, in my PDB file I specified the atomnames as per the OPLS forcefield.
I looked at the aminoacid.rtp file for the atomnames. A random residue name was assigned in the PDB file, by me.
I ran x2top (instead of pdb2gmx) with OPLS in -ff option (copied it to my working directory). I got the following errors.
"WARNING: all CONECT records are ignored
Opening force field file ./oplsaa.ff/atomname2type.n2t
There are 23 name to type translations in file ./oplsaa.ff
Generating bonds from distances…
Can not find forcefield for atom NZ-1 with 4 bonds
Can not find forcefield for atom CA-3 with 4 bonds
Can not find forcefield for atom CG-5 with 3 bonds
Can not find forcefield for atom CA-19 with 4 bonds
Can not find forcefield for atom CB-23 with 3 bonds
Can not find forcefield for atom SG-24 with 0 bonds
Can not find forcefield for atom HG-25 with 0 bonds
Can not find forcefield for atom CA-30 with 4 bonds
Can not find forcefield for atom CG-31 with 3 bonds
Fatal error:
Could only find a forcefield type for 27 out of 36 atoms"
I am a beginner to GROMACS. I tried searching the topics and the documentation. But couldnt understand. Requesting your help. Thanks