[gmx-users] ACPYPE not working.

Sat Nov 3 09:46:26 CET 2018

Ok, I'm still using Amber16, yours is 2018. I believe that they made FATAL
error now the warning we used to have with 2016 version.

There's nothing I can do. Please, seek Amber mailing list help.

Alan

On Fri, 2 Nov 2018 at 19:03, 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
> > > > > > >
> > > > > > > * 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
> > > > > > >
> > > > > > > * For (un)subscribe requests visit
> > > > > > >
> > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users
> > > > or
> > > > > > > send a mail to gmx-users-request at gromacs.org.
> > > > > > >
> > > > > >
> > > > > >
> > > > > > --
> > > > > > *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
> > > > > >
> > > > > > * For (un)subscribe requests visit
> > > > > >
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users
> > > or
> > > > > > send a mail to gmx-users-request at gromacs.org.
> > > > > --
> > > > > 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
> > > > >
> > > > > * For (un)subscribe requests visit
> > > > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users
> > or
> > > > > send a mail to gmx-users-request at gromacs.org.
> > > >
> > > >
> > > >
> > > > --
> > > > *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
> > > >
> > > > * For (un)subscribe requests visit
> > > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users
> or
> > > > send a mail to gmx-users-request at gromacs.org.
> > > --
> > > 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
> > >
> > > * For (un)subscribe requests visit
> > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> > > send a mail to gmx-users-request at gromacs.org.
> >
> >
> >
> > --
> > *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
> >
> > * For (un)subscribe requests visit
> > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> > send a mail to gmx-users-request at gromacs.org.
> --
> 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
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.

-- 
*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