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-- Jason M. Swails > On Oct 11, 2016, at 6:08 PM, Hai Nguyen <nhai.qn.gmail.com> wrote: > > .Stefan: from Bill's comment I realize that you did not use official > ambertools distribution, didn't you? > >> -I: Adding /shared/sdoerr/Software/anaconda3/bin/../dat/leap/prep to > search path. > >> -I: Adding /Users/sdoerr/miniconda3/bin/../dat/leap/prep to search path. > > It's likely you are using ambermini from 'omnia' channel? If so, can you > try http://ambermd.org/AmberTools16-get.html > > Hai > > On Tue, Oct 11, 2016 at 6:03 PM, Bill Ross <ross.cgl.ucsf.edu> wrote: > >>> Is a bit weird that a warning in Linux becomes a crash in OSX. >> >> This is one of the joys of C code. I'm not sure what the >> miniconda/bin/tleap path is about, but on my OSX it winds up under >> amber14/bin/. This might indicate you have a weird nonstandard build. >> >> Bill >> >> >>> On 10/11/16 2:43 PM, Stefan Doerr wrote: >>> Ok thanks :) This frcmod was produced by antechamber but I will take a >> look >>> at changing the names. >>> Is a bit weird that a warning in Linux becomes a crash in OSX. >>> >>> Thanks, >>> Stefan >>> >>> On Tue, Oct 11, 2016 at 6:58 PM, Gulsevin,Alican <agulsevin.chem.ufl.edu >>> >>> wrote: >>> >>>> Perhaps a format error? Your nomenclature does not match Amber atomic >>>> names, therefore leap cannot recognize your atoms, resulting in null >> data >>>> for different parameters. Fixing atom names should help. The following >> link >>>> has the guidelines for atom nomenclature: >>>> >>>> http://ambermd.org/antechamber/gaff.html >>>> >>>> Best, >>>> Alican >>>> ________________________________________ >>>> From: Stefan Doerr <stefdoerr.gmail.com> >>>> Sent: Tuesday, October 11, 2016 12:48 PM >>>> To: amber.ambermd.org >>>> Subject: [AMBER] tleap loadamberparams failing on OSX >>>> >>>> loadamberparams ligand.frcmod >>>> quit >>>> >>>> https://gist.github.com/stefdoerr/e52980d19aa0f2f4e0983489b6422e6c >>>> Here you can find the frcmod file. >>>> >>>> =========================================================== >>>> On Linux it gives: >>>> [sdoerr.loro building-protein-ligand]$ tleap -f test.in >>>> -I: Adding /shared/sdoerr/Software/anaconda3/bin/../dat/leap/prep to >>>> search >>>> path. >>>> -I: Adding /shared/sdoerr/Software/anaconda3/bin/../dat/leap/lib to >> search >>>> path. >>>> -I: Adding /shared/sdoerr/Software/anaconda3/bin/../dat/leap/parm to >>>> search >>>> path. >>>> -I: Adding /shared/sdoerr/Software/anaconda3/bin/../dat/leap/cmd to >> search >>>> path. >>>> -f: Source test.in. >>>> >>>> Welcome to LEaP! >>>> (no leaprc in search path) >>>> Sourcing: ./test.in >>>> Loading parameters: ./benzamidine.frcmod >>>> Reading force field modification type file (frcmod) >>>> Reading title: >>>> remark goes here >>>> Unknown keyword: C.ar-C.ar- in parameter file. Perhaps a format error? >>>> Unknown keyword: C.ar-C.2-N in parameter file. Perhaps a format error? >>>> Unknown keyword: C.2-N.pl3- in parameter file. Perhaps a format error? >>>> Unknown keyword: N.pl3-C.2- in parameter file. Perhaps a format error? >>>> Unknown keyword: H -N.2-H in parameter file. Perhaps a format error? >>>> Quit >>>> >>>> ============================================================ >>>> On OSX El Capitan it gives: >>>> >>>> sdoerrs-iMac:tmp2wv3g82n sdoerr$ tleap -f tleap.in >>>> >>>> -I: Adding /Users/sdoerr/miniconda3/bin/../dat/leap/prep to search >> path. >>>> >>>> -I: Adding /Users/sdoerr/miniconda3/bin/../dat/leap/lib to search path. >>>> >>>> -I: Adding /Users/sdoerr/miniconda3/bin/../dat/leap/parm to search >> path. >>>> >>>> -I: Adding /Users/sdoerr/miniconda3/bin/../dat/leap/cmd to search path. >>>> >>>> -f: Source tleap.in. >>>> >>>> >>>> Welcome to LEaP! >>>> >>>> (no leaprc in search path) >>>> >>>> Sourcing: ./tleap.in >>>> >>>> Loading parameters: ./benzamidine.frcmod >>>> >>>> Reading force field modification type file (frcmod) >>>> >>>> Reading title: >>>> >>>> Benzamidine forcefield params >>>> >>>> /Users/sdoerr/miniconda3/bin/tleap: line 19: 1008 Abort trap: 6 >>>> $AMBERHOME/teLeap -I$AMBERHOME/../dat/leap/prep >>>> -I$AMBERHOME/../dat/leap/lib -I$AMBERHOME/../dat/leap/parm >>>> -I$AMBERHOME/../dat/leap/cmd $* >>>> >>>> >>>> And it crashes. Do you know maybe what could cause this? >>>> _______________________________________________ >>>> AMBER mailing list >>>> AMBER.ambermd.org >>>> http://lists.ambermd.org/mailman/listinfo/amber >>>> >>>> _______________________________________________ >>>> AMBER mailing list >>>> AMBER.ambermd.org >>>> http://lists.ambermd.org/mailman/listinfo/amber >>>> >>> _______________________________________________ >>> AMBER mailing list >>> AMBER.ambermd.org >>> http://lists.ambermd.org/mailman/listinfo/amber >> >> >> _______________________________________________ >> AMBER mailing list >> AMBER.ambermd.org >> http://lists.ambermd.org/mailman/listinfo/amber >> > _______________________________________________ > AMBER mailing list > AMBER.ambermd.org > http://lists.ambermd.org/mailman/listinfo/amber _______________________________________________ AMBER mailing list AMBER.ambermd.org http://lists.ambermd.org/mailman/listinfo/amberReceived on Wed Oct 12 2016 - 05:30:03 PDT