AMBER Archive (2004)

Subject: Re: AMBER: segmentation fault

From: Scott Brozell (sbrozell_at_scripps.edu)
Date: Mon Mar 22 2004 - 20:10:27 CST

Hi,

A workaround is
set default PBradii bondi
before the saveAmberParm command.
The patch will come soon.

Scott Brozell

On Fri, 19 Mar 2004, Hailong Lin wrote:

> 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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