Re: [AMBER] antechamber & parmck2

From: Gustaf Olsson <>
Date: Thu, 10 Sep 2020 06:49:53 +0000

So you are technically working on the cluster when running the commands, ssh connected from a linux station terminal and from a mac terminal?

Connecting over SSH from your linux machine produces the error and connecting from mac does not?

This is somewhat surprising as you are technically working on the server and not on your local workstation. Are there any other differences in the setup? Are the systems configured with different languages, are there any other particular settings changed in the SSH connection protocol?

As you are running the commands on the server, they should all be stored in history. If you login from your mac, where the command(s) work, and try to execute the “non-working” command previously executed from the Linux machine, does it work?

    $ history | grep antechamber

In the printout you should be able to rather quickly compare if there are any visual differences and copy and execute one of the older commands which failed to execute to see if it works now.

I am not a an expert in any way or form though just from the sound of it, my guess would be a language/locale or some other “format” problem.

Best regards
// Gustaf

> On 9 Sep 2020, at 16:12, Lod King <> wrote:
> 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 <> 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 <> 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 Thu Sep 10 2020 - 00:00:02 PDT
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