[gmx-users] acpype

[Bhupendra Dandekar]

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
>> > >
>> > > * 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.
>
>