I’m trying to generate parameter files for a protein.
lteap generates top and crd files for the COMPLEX. The complex has two ligands and one water molecule
saveamberparm COMPLEX 3n7h_de4.top 3n7h_de4.crd
Checking Unit.
WARNING: The unperturbed charge of the unit: -9.002004 is not zero.
-- ignoring the warning.
Building topology.
Building atom parameters.
Building bond parameters.
Building angle parameters.
Building proper torsion parameters.
Building improper torsion parameters.
total 406 improper torsions applied
Building H-Bond parameters.
Incorporating Non-Bonded adjustments.
Not Marking per-residue atom chain types.
Marking per-residue atom chain types.
(Residues lacking connect0/connect1 -
these don't have chain types marked:
res total affected
CVAL 1
DE3 1
DE4 1
NASP 1
WAT 1
)
(no restraints)
The receptor has one ligand and one water molecule. But when I try to load the protein and generate parameters I get. Any suggestions how to overcome this problem would be most welcome
/Programs/amber12/bin/tleap: line 17: 1888 Segmentation fault: 11 $AMBERHOME/bin/teLeap -I$AMBERHOME/dat/leap/prep -I$AMBERHOME/dat/leap/lib -I$AMBERHOME/dat/leap/parm -I$AMBERHOME/dat/leap/cmd $*
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Received on Mon Dec 01 2014 - 12:00:02 PST
