AMBER Archive (2009)

Subject: Re: [AMBER] Antechamber and Parmchk problems

From: case (case_at_biomaps.rutgers.edu)
Date: Wed Nov 04 2009 - 09:26:03 CST

On Wed, Nov 04, 2009, cyk5056 wrote:

> I am using antechamber to prepare a prep file for a residue: TMS.pdb.
> $AMBERHOME/exe/antechamber -i TMS.pdb -fi pdb -o TMS.prep -fo prepc -c bcc
> It works for my computer(call it Computer 1). However, when running using another's computer(Call it computer 2), It shows:
> Total number of electrons: 198; net charge: 0
> Running: /home/na3m/Download/AMBER10/amber10/bin/mopac.sh
> Error: unable to find mopac charges in mopac.out

You need to examine the mopac.out file to find out what went wrong.
>
> For parmchk: I continue my work on Computer 1:
> $AMBERHOME/exe/parmchk -i TMS.prep -fi prepc -o TMS.frcmod

Since the previous step did not complete successfully, it is likely the
TMS.prep file is empty, or does not have good information in it. It should
probably give a better error message, but the reality is you can't continue
with the parmchk step until the original antechamber step completes
successfully.

...dac

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