AMBER Archive (2009)

Subject: Re: Re: [AMBER] Antechamber and Parmchk problems

From: cyk5056 (
Date: Wed Nov 04 2009 - 14:37:55 CST

Yeah, thank you very much!
It is strange, that TMS.prep is generated by:
$AMBERHOME/exe/antechamber -i TMS.pdb -fi pdb -o TMS.prep -fo prepc -c bcc
why does it turn out to be a mol2 file?


发件人: Junmei Wang
发送时间: 2009-11-05 03:22:49
收件人: AMBER Mailing List
主题: Re: [AMBER] Antechamber and Parmchk problems

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.
On Wed, Nov 4, 2009 at 9:26 AM, case <> 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/
> > 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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