[gmx-users] acpype

[Alan]

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