[gmx-users] ACPYPE not working.

Thu Nov 1 23:05:34 CET 2018

Please, post here the command you're using (add -d anyway for debug) and
show the whole output.

Thanks,

Alan

On Thu, 1 Nov 2018 at 20:04, neelam wafa <neelam.wafa at gmail.com> wrote:

> Yes it the same one. And the tests are running okay. Problem is with my
> files.
>
> On Fri, 2 Nov 2018, 12:56 am Alan <alanwilter at gmail.com wrote:
>
> > 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
> > > > > --
> > > > > Gromacs Users mailing list
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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
> > > > --
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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
> > --
> > Gromacs Users mailing list
> >
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> > posting!
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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