Re: [AMBER] antechamber & parmck2

From: Gustaf Olsson <>
Date: Wed, 9 Sep 2020 07:20:13 +0000

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 <> 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
> -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 Wed Sep 09 2020 - 00:30:03 PDT
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