Try using the latest ACPYPE from
https://github.com/alanwilter/acpype
On Mon, 17 Dec 2018 at 05:11, Seketoulie Keretsu <sekekeretsu.gmail.com>
wrote:
> 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
> > >>
> > >> _______________________________________________
> > >> AMBER mailing list
> > >> AMBER.ambermd.org
> > >> http://lists.ambermd.org/mailman/listinfo/amber
> > >> _______________________________________________
> > >> AMBER mailing list
> > >> AMBER.ambermd.org
> > >> http://lists.ambermd.org/mailman/listinfo/amber
> > > _______________________________________________
> > > AMBER mailing list
> > > AMBER.ambermd.org
> > > http://lists.ambermd.org/mailman/listinfo/amber
> > >
> >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Alan Wilter SOUSA da SILVA, DSc
Senior Bioinformatician, UniProt
European Bioinformatics Institute (EMBL-EBI)
European Molecular Biology Laboratory
Wellcome Trust Genome Campus
Hinxton
Cambridge CB10 1SD
United Kingdom
Tel: +44 (0)1223 494588
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Mon Dec 17 2018 - 01:30:03 PST
