thanks alot. after i changed the atomic name to 'Va', amber recognized the
vanadium.
Buuuuut, ' Segmentation Fault' is still staying where she was without any
warnings in the leap.log file.
the last several lines in leap.log may imply sth, but i cant figure out.
they are:
>> saveAmberParm alien prmtop.wat prmcrd.wat
Checking Unit.
WARNING: The unperturbed charge of the unit: -1.000000 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.
** Warning: No sp2 improper torsion term for O2-O2-VA-O2
atoms are: O1 O2 VA O4
total 1974 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)
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Received on Fri Mar 19 2004 - 12:53:00 PST
