AMBER Archive (2009)

Subject: Re: [AMBER] Antechamber and Parmchk problems

From: Junmei Wang (junmwang_at_gmail.com)
Date: Wed Nov 04 2009 - 13:21:25 CST

The attached TMS.prep is actually a mol2 file. This is the reason why
parmchk does not work.

The correct command should be: parmchk -i TMS.prep -f mol2 -o TMP.frcmod

I found all the parameters are available for this molecule.

Best

Junmei

On Wed, Nov 4, 2009 at 9:26 AM, case <case_at_biomaps.rutgers.edu> wrote:

> 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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