GROMACS version: 2020.1
GROMACS modification: No
I am working with a structure which when run via pdb2gmx to create a topology file, has a mass of 71794 and only 27071 dihedrals . When I convert the same PDB to a gro file (via editconf) and then run pdb2gmx with this gro file, the numbers increase drastically: 1050483.282 mass and 396893 dihedrals . Why is this happening?
PDB file creates some issues like throwing this error- " The residues in the chain ARG178–ATP1003 do not have a consistent type. The first residue has type ‘Protein’, while residue ATP1001 is of type ‘Other’. Either there is a mistake in your chain, or it includes nonstandard residue names that have not yet been added to the residuetypes.dat file in the GROMACS library directory ." and then crashes . For getting rid of this error, I converted the PDB to a gro and started pdb2gmx. When it didn’t complete even in 4 hours (with PDB it takes only 10 minutes), I cross-checked and came across the mass and charge and dihedrals (all stats increased) issue. Why is this happening? Please guide me through this.