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?
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>
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Received on Tue Oct 11 2016 - 15:00:02 PDT
