[gmx-users] ACPYPE not working.

Fri Nov 2 20:04:51 CET 2018

If I don't use -d then this is the result:
| ACPYPE: AnteChamber PYthon Parser interfacE v. 2018-09-20T16:44:17UTC (c)
2018 AWSdS |
========================================================================================
WARNING: no 'babel' executable, no PDB file as input can be used!
ACPYPE FAILED: [Errno 2] No such file or directory: 'tmp'
Total time of execution: less than a second

Regards

On Fri, Nov 2, 2018 at 7:02 PM neelam wafa <neelam.wafa at gmail.com> wrote:

> Hi!
> This is the command I use
> dr at dr-HP-1000-Notebook-PC:~/Downloads/acpype/test$ ../acpype.py -di
> H16.mol2 -c gas
> and the output is:
> | ACPYPE: AnteChamber PYthon Parser interfacE v. 2018-09-20T16:44:17UTC
> (c) 2018 AWSdS |
>
> ========================================================================================
> DEBUG: Python Version 3.4.3 (default, Nov 28 2017, 16:41:13)
> [GCC 4.8.4]
> DEBUG: Max execution time tolerance is 10h
> WARNING: no 'babel' executable, no PDB file as input can be used!
> DEBUG: /home/dr/Downloads/amber18/bin/antechamber -i H16.mol2 -fi mol2 -o
> tmp -fo ac -pf y
> DEBUG:
> Welcome to antechamber 17.3: molecular input file processor.
>
> acdoctor mode is on: check and diagnosis problems in the input file.
> -- Check Format for mol2 File --
>    Status: pass
> -- Check Unusual Elements --
>    Status: pass
> -- Check Open Valences --
>    Status: pass
> -- Check Geometry --
>       for those bonded
>       for those not bonded
>    Status: pass
> -- Check Weird Bonds --
> /home/dr/Downloads/amber18/bin/to_be_dispatched/antechamber: Fatal Error!
> Weird atomic valence (3) for atom (ID: 2, Name: C1).
>        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
>
> Looking forward for your suggestions
> Regards
>
> On Thu, Nov 1, 2018 at 10:05 PM Alan <alanwilter at gmail.com> wrote:
>
>> 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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>> > > > >
>> > > > >
>> > > > > --
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>> > > > > --
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>> > > > > Senior Bioinformatician, UniProt
>> > > > > European Bioinformatics Institute (EMBL-EBI)
>> > > > > European Molecular Biology Laboratory
>> > > > > Wellcome Trust Genome Campus
>> > > > > Hinxton
>> > > > > Cambridge CB10 1SD
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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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>> > --
>> > 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
>> --
>> Gromacs Users mailing list
>>
>> * Please search the archive at
>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
>> posting!
>>
>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
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>
>