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 <[email protected]> wrote: > Hi! > This is the command I use > dr@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 <[email protected]> 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 <[email protected]> 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 <[email protected] 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 <[email protected]> >> wrote: >> > > >> > > > Means this file worked well on your system? >> > > > >> > > > On Fri, 2 Nov 2018, 12:38 am Alan <[email protected] 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 <[email protected]> >> > > 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 [email protected]. >> > > > -- >> > > > 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 [email protected]. >> > > >> > > >> > > >> > > -- >> > > *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 [email protected]. >> > -- >> > 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 [email protected]. >> >> >> >> -- >> *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 [email protected]. > > -- 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 [email protected].
