[gmx-users] acpype

[Alan]

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
> >> --
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> >
> >
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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