[gmx-users] acpype

[Alan]

Latest acpype is here: https://github.com/alanwilter/acpype

Mind that it's *only* Python 3 compatible now.

Run something like this, at first, to be sure:

_full_to_your_python3 _full_path_to_acpype -d -i ...

You need Antechamber (from Amber) if you want to generate topologies.

Only if converting from Amber to GMX that you do not need Antechamber (but
if you play with AMBER format, you certainly have AmberTools installed,
right?)

I hope it helps,

Alan

On Wed, 24 Oct 2018 at 09:31, 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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Alan Wilter SOUSA da SILVA, DSc
Senior Bioinformatician, UniProt
European Bioinformatics Institute (EMBL-EBI)
European Molecular Biology Laboratory
Wellcome Trust Genome Campus
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