[gmx-users] ACPYPE not working.

[Alan]

Indeed, it worked, though the warning is important. Are you using the
latest ACPYPE?

========================================================================================
| ACPYPE: AnteChamber PYthon Parser interfacE v. 2018-09-20T16:44:17UTC (c)
2018 AWSdS |
========================================================================================


On Thu, 1 Nov 2018 at 19:46, neelam wafa <neelam.wafa at gmail.com> wrote:

> 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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> > for a charity, would you consider​ ​supporting my​ cause?
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> > --
> > Alan Wilter SOUSA da SILVA, DSc
> > Senior Bioinformatician, UniProt
> > European Bioinformatics Institute (EMBL-EBI)
> > European Molecular Biology Laboratory
> > Wellcome Trust Genome Campus
> > Hinxton
> > Cambridge CB10 1SD
> > United Kingdom
> > Tel: +44 (0)1223 494588
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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?
http://uk.virginmoneygiving.com/AlanSilva
--
Alan Wilter SOUSA da SILVA, DSc
Senior Bioinformatician, UniProt
European Bioinformatics Institute (EMBL-EBI)
European Molecular Biology Laboratory
Wellcome Trust Genome Campus
Hinxton
Cambridge CB10 1SD
United Kingdom
Tel: +44 (0)1223 494588