[gmx-users] ACPYPE not working.

[Ali Khodayari]

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
> -- 
> 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.