[gmx-users] ACPYPE not working.

[neelam wafa]

Means this file worked well on your system?

On Fri, 2 Nov 2018, 12:38 am Alan <alanwilter at gmail.com wrote:

> 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
> DEBUG:
> 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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>
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> Alan Wilter SOUSA da SILVA, DSc
> Senior Bioinformatician, UniProt
> European Bioinformatics Institute (EMBL-EBI)
> European Molecular Biology Laboratory
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