AMBER Archive (2009)

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

From: cyk5056 (cyk5056_at_163.com)
Date: Wed Nov 04 2009 - 13:56:32 CST

For parmchk, I use same TMS.prep for both of two computers and this prep file is generated without problems, which is attached in the former mail. It just shows "memory fault"..... That is the very problem

Thanks!




cyk5056
2009-11-05



发件人： case
发送时间： 2009-11-04 23:27:33
收件人： AMBER Mailing List
抄送：
主题： Re: [AMBER] Antechamber and Parmchk problems

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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