[gmx-users] segmentation fault : g_sas
magashe at CLEMSON.EDU
Thu Feb 19 16:01:02 CET 2004
How can I get a bug free version of g_sas?
The index file does correspond to the tpr/xtc.
From: gmx-users-admin at gromacs.org [mailto:gmx-users-admin at gromacs.org] On
Behalf Of David van der Spoel
Sent: Wednesday, February 18, 2004 4:55 PM
To: gmx-users at gromacs.org
Subject: RE: [gmx-users] segmentation fault : g_sas
On Wed, 18 Feb 2004, Madhuri Agashe wrote:
>G_sas gives segmentation fault but not everytime, it is rather erratic in
>behavior. It ran fine for one group in the index file. When I tried it on
>another group, g_sas gave a segmentation fault again.
>My command was simply
>g_sas -f 3.xtc -s 3.tpr -n 6.ndx -o p1.xvg
that version of g_sas is probably full of bugs.
otherwise you might check the index file, to see whether it corresponds to
>my version of gromacs is 3.1.3
>has anyone else faced a similar problem???
>From: gmx-users-admin at gromacs.org [mailto:gmx-users-admin at gromacs.org] On
>Behalf Of David
>Sent: Saturday, January 31, 2004 3:57 AM
>To: gmx-users at gromacs.org
>Subject: Re: [gmx-users] segmentation fault : g_sas
>On Sat, 2004-01-31 at 01:13, Madhuri Agashe wrote:
>> I am trying to analyze the solvent accessible areas for a protein after
>> running molecular dynamics on it.
>> I used the following command:
>> g_sas -f 2.trr -s 2.tpr -o area.xvg -r resarea.xvg -n 3.ndx
>> I always get the following output for this:
>> Opening library file /usr/local/share/gromacs/top/dgsolv.dat
>> ++++++++ PLEASE CITE THE FOLLOWING REFERENCE ++++++++
>> D. Eisenberg and A. D. McLachlan
>> Solvation energy in protein folding and binding
>> Nature 319 (1986) pp. 199-203
>> -------- -------- --- Thank You --- -------- --------
>> 3987 out of 70695 atoms were classified as hydrophobic
>> Back Off! I just backed up area.xvg to ./#area.xvg.3#
>> frame: 0Segmentation fault
>> Is this segmentation fault due to some error in any of the input files?
>> is there some problem with this command?
>does it also crash with the -r option?
>which gromacs version?
>is 3.ndx correct?
>> gmx-users mailing list
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David van der Spoel, PhD, Assist. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596, 75124 Uppsala, Sweden
phone: 46 18 471 4205 fax: 46 18 511 755
spoel at xray.bmc.uu.se spoel at gromacs.org http://xray.bmc.uu.se/~spoel
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