AMBER Archive (2009)

Subject: Re: [AMBER] Segmentation fault in antechamber

From: Scott Brozell (sbrozell_at_rci.rutgers.edu)
Date: Mon Dec 14 2009 - 23:34:39 CST

Hi,

Fixed for the upcoming AmberTools 1.3 release.
The behavior is to emit:
Warning: detected more than ten Residue sequence numbers;
    this may be a large multiple residue PDB file;
    large multiple residue PDB files are not supported.
    Continuing, but problems may be encountered.

Also some memory management issues were fixed, but large
multiple residue PDB files may still cause crashes.

Scott

> On Wed, Nov 18, 2009 at 5:28 AM, case <case_at_biomaps.rutgers.edu> wrote:
> > > On Tue, Nov 17, 2009, albert albert wrote:
> > > The pdb is linked.
> >
> > The idea is that you give a pdb-formatted file for a *single residue* or a
> > small organic molecule to antechamber. It looks like you tried to feed it
> > an
> > entire pdb file with several hundred residues(?). Of course, this should
> > provide a better error message, but it will never work.

On Mon, Nov 16, 2009 at 04:28:20PM +0100, albert albert wrote:
> I receive segmentation fault, after the launch of the following command of
> antechamber.
> antechamber -i cpc.pdb -fi pdb -o cpc.mol2 -fo mol2 -c bcc -s 2
> Segmentation
> Someone can help to know the source of this error and how can I solve it.

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