GROMACS version: 2023
GROMACS modification: No
I have 2 simulated proteins which I merged in order to study its conformation mechanism and learn its trajectory. The issue that I am facing is, the merged files need to be directly sent out for equilibration and production run. Problem arising is that I am unable to create its .top file.
Used cmd, gmx pdb2gmx -f —.pdb -o topol.top which is not processing, took more than 12 hrs so I had to terminate.
Tried clearing the water mols and ions and tried to create an input file with Charmm but again it shows the error “Error parsing ATOM, expected chain ID at column 22, but got ’ ’ : ATOM 1 N ALA ^ 1 87.090 62.700 4.760 0.00 0.00 N”
Also, upon trying to generate topology using pdb2gmx and using OPLS FF, it gives an error “Residue HSD not found in residue topology file” which on checking was present., source file: src/gromacs/gmxpreprocess/resall.cpp (line 616)
I am fairly new to using Gromacs and computational sciences as you can tell. Kindly help with resolving this issue.
Million thanks in advance :')