[gmx-users] acpype

[Bhupendra Dandekar]

Thanks to you also sir.
Your work is really appreciated and is really helpful.


Bhupendra

On Wed, Oct 24, 2018 at 3:59 PM Alan <alanwilter at gmail.com> wrote:

> Thanks Bhupendra, indeed we have this option, which is experimental, but
> I'm glad to see some are already using it and it seems to be working.
>
> Alan
>
> On Wed, 24 Oct 2018 at 11:20, Bhupendra Dandekar <
> bhupendra.dandekar001 at gmail.com> wrote:
>
> > Dear Farial,
> >
> > Use this command to install acpype and antechamber using conda:
> >
> > conda install -c acpype -c openbabel -c ambermd
> >
> > and then you can check and call acpype, antechamber like this from your
> > terminal:
> >
> > acpype -h
> > antechamber -h
> >
> > then you can generate ligand topology using this command:
> >
> > acpype -i FFF.pdb -b FFF -o gmx
> >
> > Hope this helps. Let me know if you have any questions.
> >
> > Thanks
> > Bhupendra
> >
> > On Wed, Oct 24, 2018 at 2:01 PM Farial Tavakoli <
> faryal.tavakoli at gmail.com
> > >
> > wrote:
> >
> > > Dear GMX useres
> > >
> > > I am trying to convert .OFF and .FRCMOD files obtained from AMBER
> > parameter
> > > database (Bryce Group: Computational Biophysics and Drug Design -
> > > University of Manchester)
> > > <http://sites.pharmacy.manchester.ac.uk/bryce/amber> to the format
> that
> > > GROMACS is compatible with in .rtp files*. so referred to GROMACS
> > tutorial
> > > protein-ligand complex and downloaded acpype. installed it using its
> > > readme.txt file but whenever i typed    ../acpype.py -i FFF.pdb   At
> > folder
> > > *acpype/test*   (/Downloads/acpype-master/acpype) or
> > > (/Downloads/acpype-master/acpype/test) faced to this error:*
> > >
> > >
> > > *bash: ../acpype.py: No such file or directory*
> > >
> > > *while when I typed whereis acpype in terminal , the operating system
> > says
> > > :*
> > >
> > >
> > > *acpype: /usr/local/bin/acpype*
> > > * it means there is the executable file of acpype . so how come I type
> > > ../acpype.py -h or ../acpype -i FFF.pdb , the system says NO such file
> or
> > > directory?*
> > > *Is there anyone who ca help me?*
> > > *I really would be appreciated it if one help me to solve this and can
> > > convert the AMBER format files to GRMACS format files.*
> > >
> > > *best regards*
> > > *Farial*
> > > --
> > > Gromacs Users mailing list
> > >
> > > * Please search the archive at
> > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > > posting!
> > >
> > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> > >
> > > * For (un)subscribe requests visit
> > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> > > send a mail to gmx-users-request at gromacs.org.
> > >
> > --
> > Gromacs Users mailing list
> >
> > * Please search the archive at
> > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > posting!
> >
> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >
> > * For (un)subscribe requests visit
> > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> > send a mail to gmx-users-request at gromacs.org.
> >
>
>
> --
> *I**​ have just cycled* from Land's End to John O'Groats​​​ (the
> whole Britain!)
> for a charity, would you consider​ ​supporting my​ cause?
> http://uk.virginmoneygiving.com/AlanSilva
> --
> 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
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.