AMBER Archive (2004)

Subject: Re: AMBER: segmentation fault

From: Hailong Lin (
Date: Fri Mar 19 2004 - 06:41:50 CST

thanks alot. after i changed the atomic name to 'Va', amber recognized the
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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