Dear Bill,
Thanks for the idea. sound little scary but will do that and see. I
have also reframed the question and posted on the forums just to see
if someone out there miraculously got it.
Best, Seke
On Mon, Dec 17, 2018 at 11:48 AM Bill Ross <ross.cgl.ucsf.edu> wrote:
>
> Hi Seke,
>
> I'd try adding a '2' tp 'parmchk' in whatever script is running, and if
> it seems to work watch for other problems in case usage or assumptions
> have changed. I'm not familiar with the code myself, but you may find
> useful discussion in the archives.
>
> Bill
>
> On 12/16/18 4:31 PM, Seketoulie Keretsu wrote:
> > Dear Bill,
> >
> > Thank you for the response. I have executed the environment setup
> > script (sanders, tleap etc can be called from console). I noticed in
> > the error report that "parmchk" has failed. Interestingly, in
> > Amber2018 (i.e $AMBERHOME/bin) the "parmchk2" is available not
> > "parmchk". Hence if acpype is looking for parmchk, this could be a
> > problem. I could be very wrong. Kindly advise.
> >
> > The error report is shown below:
> > ++++++++++start_quote+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
> > /bin/sh: -c: line 0: syntax error near unexpected token `('
> > /bin/sh: -c: line 0: `which: no parmchk in
> > (/home/main/Downloads/amber18/bin:/home/main/Downloads/amber18/bin:/usr/lib64/qt-3.3/bin:/usr/local/bin:/usr/local/sbin:/usr/bin:/usr/sbin:/bin:/sbin:/usr/local/gromacs/bin:/home/main/.local/bin:/home/main/bin:/usr/local/gromacs/bin)
> > -i Ligand_bcc_gaff.mol2 -f mol2 -o Ligand_AC.frcmod'
> > ++++++++++end_quote+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
> > ERROR: Parmchk failed
> > ERROR: Tleap failed
> > ==> ... trying Sleap
> > ==> Executing Sleap...
> > ++++++++++start_quote+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
> >
> > Thank you. Seke
> >
> > On Sun, Dec 16, 2018 at 11:10 PM Bill Ross <ross.cgl.ucsf.edu> wrote:
> >> Did you run the environment setup script? amber.sh for bash I think.
> >>
> >> Bill
> >>
> >> <div>-------- Original message --------</div><div>From: Seketoulie Keretsu <sekekeretsu.gmail.com> </div><div>Date:12/16/2018 5:58 AM (GMT-08:00) </div><div>To: amber.ambermd.org </div><div>Subject: [AMBER] Acpype related problem : topology for GROMACS </div><div>
> >> </div>Dear Expert,
> >>
> >> I came this problem while trying to generate ligand topology for use Gromacs.
> >> I have gromacs 2018 and also amber installed in my system (CentOS7).
> >>
> >> I installed acpype by extracting the .tar file and "python setup.py install".
> >>
> >> I am following the tutorial give in this link:
> >> https://code.google.com/archive/p/acpype/wikis/TutorialAcpype4Gromacs.wiki
> >>
> >> The error report is shown below.
> >>
> >> [main.localhost try1]$ acpype -i Ligand.pdb
> >> ============================================================================
> >> | ACPYPE: AnteChamber PYthon Parser interfacE v. 0 0 Rev: 0 (c) 2018 AWSdS |
> >> ============================================================================
> >> ==> ... charge set to 0
> >> ==> ... converting pdb input file to mol2 input file
> >> ==> * Babel OK *
> >> ==> Executing Antechamber...
> >> ==> * Antechamber OK *
> >> ++++++++++start_quote+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
> >> /bin/sh: -c: line 0: syntax error near unexpected token `('
> >> /bin/sh: -c: line 0: `which: no parmchk in
> >> (/home/main/Downloads/amber18/bin:/home/main/Downloads/amber18/bin:/usr/lib64/qt-3.3/bin:/usr/local/bin:/usr/local/sbin:/usr/bin:/usr/sbin:/bin:/sbin:/usr/local/gromacs/bin:/home/main/.local/bin:/home/main/bin:/usr/local/gromacs/bin)
> >> -i Ligand_bcc_gaff.mol2 -f mol2 -o Ligand_AC.frcmod'
> >> ++++++++++end_quote+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
> >> ERROR: Parmchk failed
> >> ERROR: Tleap failed
> >> ==> ... trying Sleap
> >> ==> Executing Sleap...
> >> ++++++++++start_quote+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
> >>
> >> ++++++++++end_quote+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
> >> ++++++++++start_quote+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
> >> /bin/sh: -c: line 0: syntax error near unexpected token `('
> >> /bin/sh: -c: line 0: `which: no sleap in
> >> (/home/main/Downloads/amber18/bin:/home/main/Downloads/amber18/bin:/usr/lib64/qt-3.3/bin:/usr/local/bin:/usr/local/sbin:/usr/bin:/usr/sbin:/bin:/sbin:/usr/local/gromacs/bin:/home/main/.local/bin:/home/main/bin:/usr/local/gromacs/bin)
> >> -f sleap.in'
> >>
> >> ++++++++++end_quote+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
> >> ERROR: Sleap failed
> >> ==> Removing temporary files...
> >> ACPYPE FAILED: [Errno 2] No such file or directory: 'Ligand_AC.prmtop'
> >> Total time of execution: 12m 43s
> >>
> >> What could be the problem here and how do i rectify this ??
> >>
> >> Thank you.
> >>
> >> Sincerely, Seke
> >>
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Received on Sun Dec 16 2018 - 21:30:04 PST
