Yes it reran it and now it works. Seems like my mol2 had sybyl atomtypes.
Now it works.
Thanks!
On Wed, Oct 12, 2016 at 2:09 PM, Jason Swails <jason.swails.gmail.com>
wrote:
> Atom names must be 2 letters or fewer. Mol2 files should be prepared by
> antechamber before using as a library file in tleap.
>
> Your atom types are standard mol2 types, suggesting that you did not run
> your molecule through antechamber to get charges and atom types first.
>
> HTH,
> Jason
>
> --
> 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
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> > http://lists.ambermd.org/mailman/listinfo/amber
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Received on Wed Oct 12 2016 - 06:30:02 PDT
