GROMACS version: 2021.4
GROMACS modification: Yes/No
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I used Acpype to generate a topology file for my protein. I try to run energy minimization, but get a syntax error saying invalid order of directives GROMACS can’t read the Acpype generated topology file. If I try to delete the extra lines Acpype provides that specify the conversion names of atoms between Amber and GROMACS, the defaults and atomtypes lines. GROMACS will not understand the atoms in the topology file. I am stuck because I can’t perform em step because Acpype wrote the topology format in the wrong way, but what it wrote is necessary for GROMACS to understand the specific atoms in the topology file.
It is how the atoms and residues are named which is in AMBER format (CYS is CYX). GROMACS is having trouble reading the atoms and residues in the topology. I am using amber99sb force-field.
What is the Calcium ion named in the topology database?
I figured it out.
HETATM 3869 CA CA 259 20.380 18.050 23.490 1.00 0.00 Ca
For calcium, it is CA and Ca in the pdb file with the protein.
what is your pdb id?
In my (extremely limited) experience with acpype, the topology you get for the molecule you parameterize has first the [ atomtypes ] section, as the molecule will need specific new atom types, and then the [ moleculetype ] section (and the following ones) that form the true topology of the molecule.
If this is the case, then GROMACS doesn’t want two [ atomtypes ] sections (the one from the force field and the one from the acpype topology) and you have to append by hand the [ atomtypes ] entries in the acpype generated topology to the force field ones.
Also, isn’t acpype mostly for ligands (gaff/gaff2 parameters)? For a protein I would use standard amber of some kind (amber99sb etc.).