[gmx-users] ACPYPE not working.

[neelam wafa]

Yes i have sourced antechamber and both antechamber -h and acpype -h
command work. When i run command
acpype.py -i ligand.mol2
It says  no such file or directory 'temp'
With acpype.py -di ligand.mol2 its gives above error.

On Thu, 1 Nov 2018, 4:46 pm Ali Khodayari <ali.khodayari at student.kuleuven.be
wrote:

> Have you tried to source amber before commanding acpype for the conversion?
> Apparently it’s looking for antechamber but it can’t access it.
> When amber is sourced first, you can get a result from commands such as
> antechamber -h
> Try to first source your amber, and then run acpype.
>
> > On 1 Nov 2018, at 09:52, neelam wafa <neelam.wafa at gmail.com> wrote:
> >
> > Hi!
> > Dear all
> > I am using acpype to generate topologies of ligand for gromacs md
> > simmulation. I habe amber tools 18 and downloaded acpype from github. The
> > test runs go well but when i run my file with  ../acpype.py -i UNL.mol2
> -c
> > gas or even
> > ../acpype.py -di UNL.mol2
> > iI get following error
> > /home/dr/Downloads/amber18/bin/to_be_dispatched/antechamber: Fatal Error!
> > Weird atomic valence (2) for atom (ID: 1, Name: C).
> >       Possible open valence.
> > ACPYPE FAILED: [Errno 2] No such file or directory: 'tmp'
> >  File "../acpype.py", line 3704, in <module>
> >  File "../acpype.py", line 3392, in __init__
> >  File "../acpype.py", line 910, in setResNameCheckCoords
> > Total time of execution: less than a second
> > Please any way to get out of this problem? Looking forward for your
> > cooperation
> > Regards
> > --
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