[gmx-users] ACPYPE not working.

Alan alanwilter at gmail.com
Thu Nov 1 20:38:21 CET 2018

This kind of problem is due to ANTECHAMBER, not ACPYPE. You may try to get
help at AMBER mailing list.

For an example I was given, running here:
acpype -di H16.mol2 -c gas

DEBUG: /Users/alan/Programmes/amber16/bin/*antechamber* -i H16.mol2 -fi
mol2 -o tmp -fo ac -pf y
Warning: the assigned bond types may be wrong, please :
(1) double check the structure (the connectivity) and/or
(2) adjust atom valence penalty parameters in APS.DAT, and/or
(3) increase PSCUTOFF in define.h and recompile bondtype.c
    Be cautious, use a large value of PSCUTOFF (>100) will significantly
increase the computation time

On Thu, 1 Nov 2018 at 08:53, 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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*I**​ have just cycled* from Land's End to John O'Groats​​​ (the
whole Britain!)
for a charity, would you consider​ ​supporting my​ cause?
Alan Wilter SOUSA da SILVA, DSc
Senior Bioinformatician, UniProt
European Bioinformatics Institute (EMBL-EBI)
European Molecular Biology Laboratory
Wellcome Trust Genome Campus
Cambridge CB10 1SD
United Kingdom
Tel: +44 (0)1223 494588

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