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.w...@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 <alanwil...@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.w...@gmail.com> wrote: > > > > > Means this file worked well on your system? > > > > > > On Fri, 2 Nov 2018, 12:38 am Alan <alanwil...@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.w...@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? 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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-requ...@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-requ...@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-requ...@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-requ...@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-requ...@gromacs.org.