[gmx-users] acpype

Bhupendra Dandekar bhupendra.dandekar001 at gmail.com
Wed Oct 24 12:19:44 CEST 2018

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

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.


On Wed, Oct 24, 2018 at 2:01 PM Farial Tavakoli <faryal.tavakoli at gmail.com>

> 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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