[AMBER] antechamber & parmck2

From: Lod King <lodking407.gmail.com>
Date: Tue, 8 Sep 2020 18:25:38 -0700


I used to use the following commands to generate prepc and frcmod files.

$ antechamber -i ligand.pdb -fi pdb -o ligand.prepc -fo prepc -nc -2 -c bcc
-s 2 -at gaff2

and parmchk for the frcmod file:

$ parmchk2 -i ligand.prepc -f prepc -o ligand.frcmod -a Y

now I am able to generate ligand.prepc, but when hitting parmchk2, it
prompts me to

$ parmchk2 -i ligand.prepc -f prepc -o ligand.frcmod -a Y
Usage: parmchk2 -i input file name
                -o frcmod file name
                -f input file format (prepi, prepc, ac, mol2)
                -s ff parm set, it is suppressed by "-p" option
                    1: gaff (the default)
                    2: gaff2
                -p parmfile
                -pf parmfile format
                    1: for amber FF data file (the default)
                    2: for additional force field parameter file
                -c atom type corresponding score file, default is
                -a print out all force field parameters including those in
the parmfile
                    can be 'Y' (yes) or 'N' (no) default is 'N'
                -w print out parameters that matching improper dihedral
                    that contain 'X' in the force field parameter file, can
be 'Y' (yes)
                    or 'N' (no), default is 'Y'

Did I miss any flags?
AMBER mailing list
Received on Tue Sep 08 2020 - 18:30:03 PDT
Custom Search