> 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
>>
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>>
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Received on Tue Oct 11 2016 - 15:30:02 PDT
