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? 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.