Hello, Gustaf
If dropping "-a Y", I would get the printout with partial info missed", not
sure why.
In addition, all work was done in my Linux station, which I ssh to work at
our supercomputer station.
and Then, I switched to my mac and ssh via terminal to work at
supercomputer, everything is normal, I got the prepc and frcmod of I need,
very confused.
On Wed, Sep 9, 2020 at 12:20 AM Gustaf Olsson <gustaf.olsson.lnu.se> wrote:
> If I run the same command as you, having none of the files, I get the
> expected error
>
> Cannot open file (ligand.prepc) with mode (r).
> No such file or directory
>
> The printout presented is what I receive when running "parmchk2” without
> any input or options/flags. This would suggest an incorrect command. I
> might be going blind though I cannot se any obvious errors with the
> supplied commands.
>
> The -i, -f and -o flags are, as far as I know, the only required flags.
> What happens if you drop the “-a Y”?
>
> Best regards
> // Gustaf
>
> > On 9 Sep 2020, at 03:25, Lod King <lodking407.gmail.com> wrote:
> >
> > 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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> > http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Wed Sep 09 2020 - 07:30:03 PDT
