.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
>
>
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Received on Tue Oct 11 2016 - 15:30:03 PDT
