AMBER: segmentation fault

From: Hailong Lin <hailong.lin.stud.man.ac.uk>
Date: Thu, 18 Mar 2004 12:48:24 -0000

i am using amber7 ,working on the haloperoxidase with a Vanadium in its active site. when doing LEap, after the topology file was saved the program ended with ' Segmentaion fault (core dumped) '.
the lines at the end of the leap.log file are below:
    Building topology.
    Building atom parameters.
    Building bond parameters.
    Building angle parameters.
    Building proper torsion parameters.
    Building improper torsion parameters.
     total 1907 improper torsions applied
    Building H-Bond parameters.
    Marking per-residue atom chain types.
      (Residues lacking connect0/connect1 -
       these don't have chain types marked:

            res total affected

            CMET 1
            NSER 1
            VO4 1
            WAT 20614
      )
     (no restraints)
    Segmentation fault (core dumped)
since the amber default force field doesn't have the parameters for Vanadium.i formed my own frcmod.pcy file and use the commmand 'addAtomTypes { { "V" "V" "sp3" } } '. it seems V can not be recognized as an element name, ' atom type V - unknown element V' was printed in the leap.log file.
the frcmod.pcy file are:
# Modifications to force field for haloperoxidase
MASS
V 50.940 ! alien

BOND
V -O2 615.000 1.76000 lalala
V -N 250.000 6.56000 lala
C -V 250.000 6.56000 la
O2-H 340.000 1.09000
O2-O2 150.000 2.46048

ANGLE
O2-V -O2 100.00 105.199 lalala
O2-V -N 100.00 78.230 lala
V -N -H 100.00 153.910
V -N -CT 100.00 156.130
O -C -V 100.00 124.480
C -V -O2 100.00 72.660
C -V -N 100.00 16.010
CT-C -V 100.00 20.490
O -C -OH 100.00 60.000
CT-C -OH 100.00 60.000
V -O2-O2 100.00 40.556
V -O2-H 100.00 109.500

DIHE
O2-V -NB-CV 1 1.000 44.000 3.000
X -C -V -X 1 1.000 180.000 3.000
O2-V -N -H 1 1.000 -97.923 3.000
O2-V -N -CT 1 1.000 -48.604 3.000
C -V -N -H 1 1.000 -30.108 3.000
C -V -N -CT 1 1.000 19.211 3.000
CT-H -N3-H 1 1.000 -120.023 3.000
H -H -N3-H 1 1.000 120.015 3.000

IMPROPER
C*-CN-CB-CA 1 1.000 -179.476 3.000
NA-CA-CN-CB 1 1.000 -179.959 3.000
O2-O2-V -O2 1 1.000 -90.167 3.000
O2-V -O2-H 1 1.000 90.834 3.000
O2-V -O2-O2 1 1.000 -132.246 3.000

NONBON
  V 2.8500 0.2000 Thomas et al JPC,102,(1998),997

what can i do to get rid of the segmentation fault and let the amber accept vanadium?

cheers

hailong

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Received on Thu Mar 18 2004 - 13:53:01 PST
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