Hello AMBER
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
PARMCHK.DAT
-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
parameters
that contain 'X' in the force field parameter file, can
be 'Y' (yes)
or 'N' (no), default is 'Y'
Did I miss any flags?
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Received on Tue Sep 08 2020 - 18:30:03 PDT
