[gmx-users] acpype

Wed Oct 24 17:58:00 CEST 2018

Hi alan

Can you please tell how long will it take for the online acpype server to
be available?

Regards
Neelam wafa

On Wed, 24 Oct 2018, 6:23 pm Alan, <alanwilter at gmail.com> wrote:

> Indeed, it's mostly Luciano spearheading these new things. Hopefully, we
> will have more things to show eventually.
>
> Alan
>
> On Wed, 24 Oct 2018 at 14:14, Bhupendra Dandekar <
> bhupendra.dandekar001 at gmail.com> wrote:
>
> > I actually got lot of help from Luciano Kagami about installation and
> usage
> > of acpype and ligro.
> > Thanks to both of you.
> >
> > Bhupendra
> >
> > On Wed, Oct 24, 2018 at 6:38 PM Bhupendra Dandekar <
> > bhupendra.dandekar001 at gmail.com> wrote:
> >
> > > 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
> > >> > >
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> > >> > >
> > >> > --
> > >> > Gromacs Users mailing list
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> > >>
> > >>
> > >> --
> > >> *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
> > >>
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> > >> posting!
> > >>
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> > >>
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> > >
> > >
> > --
> > Gromacs Users mailing list
> >
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>
>
> --
> *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
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> posting!
>
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>
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