AMBER Archive (2009)

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

From: Junmei Wang (junmwang_at_gmail.com)
Date: Thu Nov 05 2009 - 15:16:51 CST

It is not necessary for you to stick on one format. The purpose of running
parmchk is to find the missing force field parameters and load them to leap.
You can use any supported formats (ac, mol2, prepi and prepc) to run
parmchk. Once you get the frcmod fiel, other formats, not necessary the one
used to run parmchk, can be loaded to leap to generate the topology files.
Good luck ...

Junmei

2009/11/5 cyk5056 <cyk5056_at_163.com>

> Actually it works for prepi. However, I need to use prepc because I need to
> edit the prep file a little. What can I do?
>
> Thank you!
>
>
>
>
> cyk5056
> 2009-11-06
>
>
>
> 发件人： Junmei Wang
> 发送时间： 2009-11-05 05:09:08
> 收件人： AMBER Mailing List
> 抄送：
> 主题： Re: Re: [AMBER] Antechamber and Parmchk problems
>
> Hi,
> I am sorry, the attached file in your previous email is a PREPC file, not a
> mol2 file. It is difficult to figure out what causes the core dump since
> the
> parmchk works for all my computers. By the way, if you convert the prepc to
> mol2 and prepi, do you still have the core dump problem with parmchk?
> Best
> Junmei
> On Wed, Nov 4, 2009 at 2:37 PM, cyk5056 <cyk5056_at_163.com> wrote:
> > 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?
> >
> >
> >
> >
> >
> > cyk5056
> > 2009-11-05
> >
> >
> >
> > 发件人： Junmei Wang
> > 发送时间： 2009-11-05 03:22:49
> > 收件人： AMBER Mailing List
> > 抄送：
> > 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.
> > 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
> > >
> > >
> > > _______________________________________________
> > > AMBER mailing list
> > > AMBER_at_ambermd.org
> > > http://lists.ambermd.org/mailman/listinfo/amber
> > >
> > _______________________________________________
> > AMBER mailing list
> > AMBER_at_ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
> > _______________________________________________
> > AMBER mailing list
> > AMBER_at_ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
> >
> _______________________________________________
> AMBER mailing list
> AMBER_at_ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
> _______________________________________________
> AMBER mailing list
> AMBER_at_ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
>
_______________________________________________
AMBER mailing list
AMBER_at_ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber