[gmx-users] acpype

Mon Oct 29 21:11:00 CET 2018

Are you running python3?

what

python -V

or

python3 -V

outputs?

Alan

On Mon, 29 Oct 2018 at 13:25, neelam wafa <neelam.wafa at gmail.com> wrote:

> Hi
> Thanks for your help. I have resolved that problem but got another one .
> when I run the command
>
> ../acpype.py -i FFF.pdb
>
> I get this error.
> File "../acpype.py", line 561
>     def __init__(self) -> None:
>                        ^
> SyntaxError: invalid syntax
>
> can you please help me out of the situation?
>
> Thanks in advance
>
> Regards
>
>
>
> On Thu, Oct 25, 2018 at 4:02 PM Alan <alanwilter at gmail.com> wrote:
>
> > Check your python3, what's the command line for your python3?
> >
> > The shebang line (first line) in acpype.py is:
> >
> > #!/usr/bin/env python3
> >
> > you need python3 to run acpype. If your default python is already
> python3,
> > then change line to
> >
> > #!/usr/bin/env python
> >
> > python -V
> >
> > tells which python version you have.
> >
> > Thanks,
> >
> > Alan
> >
> > On Thu, 25 Oct 2018 at 16:44, neelam wafa <neelam.wafa at gmail.com> wrote:
> >
> > > Hi, Alan
> > >
> > > I have installed amber tools 18 for antechamber and acpype with
> > >
> > > git clone https://github.com/alanwilter/acpype.git
> > >
> > > then installed it with
> > >  ln -s $PWD/acpype.py /usr/local/bin/acpype
> > >
> > > I didn't install open babel because my input files are in mol2 format.
> > > when i reun the command acpype -h or acpype i ligand.mol2
> > >
> > > it says, acpype command not found.
> > >
> > > please help me about how to use acpype to generate ligand topology as
> > > i have been the online acpype server for the purpose.
> > >
> > > thanks in advance.
> > >
> > > Regards
> > >
> > >
> > > On Wed, Oct 24, 2018 at 9:29 PM Alan <alanwilter at gmail.com> wrote:
> > >
> > > > We are working on it now. I can't tell you exactly because we need
> > > several
> > > > tests. It's a complete new version re-written from scratch.
> > > >
> > > > I'm really sorry for the inconvenience but we hope to bring it back
> in
> > a
> > > > month or two.
> > > >
> > > > Alan
> > > >
> > > > On Wed, 24 Oct 2018 at 16:58, neelam wafa <neelam.wafa at gmail.com>
> > wrote:
> > > >
> > > > > 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*
> > > > > > > >> > > --
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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
> > > > > > --
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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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> >
> >
> >
> > --
> > *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!
> >
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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