AMBER Archive (2005)

Subject: Re: AMBER: crashing xleap

From: Furse, Kristina Elisabet (kristina.e.furse_at_vanderbilt.edu)
Date: Fri May 20 2005 - 17:28:05 CDT

Kenley-

All of your atoms are listed as type "DU" for dummy atom, so you are getting a
residue with no atoms in it. When leap tries to create your loop, it can't find
the atoms to connect, and dies. Just go through and assign atom types and you
should be fine.

Good luck!
Kristina

Quoting Kenley Barrett <kenley.barrett_at_gmail.com>:

> Scott,
>
> Thanks for your help. I have attached the prep file. I am using Amber
> 8, and I open XLeap using the command:
>
> /opt/local/amber8/exe/xleap -s -f /opt/local/amber8/dat/leap/cmd/leaprc.ff99
>
> The first command that I then enter into XLeap is:
>
> loadamberprep himethyl_jag.prep
>
> The program immediately crashes.
>
> Please let me know if I can give you any further information.
>
> Thanks,
> Kenley
>
> On 5/20/05, Scott Brozell <sbrozell_at_scripps.edu> wrote:
> > Hi Kenley,
> >
> > I am not aware of this bug. If you send me your input files, your
> > leap.log for the commands you attempted, and some details like which
> > amber version, what computing platform, etc then I'll try to
> > reproduce your bug.
> >
> > Scott Brozell
> >
> > On Fri, 20 May 2005, Kenley Barrett wrote:
> >
> > > Amber users,
> > >
> > > I am trying to create a library file for an unusual residue. I have
> > > created a prep file, but whenever I try the XLeap command
> > > "loadamberprep [jobname].prep", XLeap immediately crashes due to a
> > > "segmentation fault". Has anyone else had this problem, and does
> > > anyone know how to fix it?
> > >
> > > Please let me know any suggestions that you have. Thank you in advance
> > > for your help.
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>

-----------------------------------------------------------------
Kristina E. Furse
Department of Chemistry
Center for Structural Biology
Vanderbilt University
Email: kristina.e.furse_at_Vanderbilt.Edu
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