Hi,
What version of AmberTools are you running, and what updates have been
applied? Do all tests pass?
-Dan
On Monday, December 1, 2014, George Tzotzos <gtzotzos.me.com> wrote:
> 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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> http://lists.ambermd.org/mailman/listinfo/amber
>
--
-------------------------
Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 307
Salt Lake City, UT 84112-5820
http://home.chpc.utah.edu/~cheatham/
(801) 587-9652
(801) 585-6208 (Fax)
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Received on Mon Dec 01 2014 - 12:30:02 PST
