Hi all,
I’m trying to set up a ‘pipeline’ that uses pdb2pqr to set receptor protonation states and then AmberTools to prepare prmtop and mol2 files. The mol2 files will be used in UCSF DOCK. I am using the following script in tleap:
source leaprc.ff14SB
set default PBRadii bondi
# Receptor
protein = loadpdb 3cqwA.0.amber.pqr
saveamberparm protein 3cqwA.0.prmtop 3cqwA.0.inpcrd
savepdb protein 3cqwA.0.amber.pdb
savemol2 protein 3cqwA.0.mol2 0 # default atom types, seems to have a bug
quit
This successfully generates prmtop, inpcrd, and pdb files. However, tleap crashes at the end of this script:
...
Writing pdb file: 3cqwA.0.amber.pdb
Converting N-terminal residue name to PDB format: NARG -> ARG
Converting C-terminal residue name to PDB format: CTHR -> THR
Writing mol2 file: 3cqwA.0.mol2
/Users/dminh/Installers/amber14/bin/tleap: line 17: 1183 Abort trap: 6 $AMBERHOME/bin/teLeap -I$AMBERHOME/dat/leap/prep -I$AMBERHOME/dat/leap/lib -I$AMBERHOME/dat/leap/parm -I$AMBERHOME/dat/leap/cmd $*
There is no further information in leap.log. Any ideas or suggestions?
David Minh, PhD
Assistant Professor of Chemistry
Illinois Institute of Technology
Research group: http://mypages.iit.edu/~dminh/
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Received on Wed Jul 23 2014 - 10:00:02 PDT
