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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Received on Tue Oct 11 2016 - 10:00:03 PDT
