[gmx-users] ACPYPE not working.

[neelam wafa]

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
> > > > --
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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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