[gmx-users] g_sas with 3.3 and 3.3.2 gives different results

[David van der Spoel]

Isabella Daidone wrote:
> Hi,
> 
> I have a box with multiple peptides in it.
> When I run g_sas either on a single peptide  or on all peptides I get 
> different results with version 3.3 and version 3.3.2
> 
> 1) On a single peptide (I chose 1 peptide for surface calculation and 1 
> peptide as the output):
> 
> with 3.3:
> # g_sas -f ../traj1_12_1micro_System_dt100ps.xtc -e 100 -s topol33.tpr 
> -o area1_33.xvg -n index.ndx
> #
>          0     1.05683     1.53052     2.58735           0
> 
> with 3.3.2
> # g_sas -f ../traj1_12_1micro_System_dt100ps.xtc -e 100 -s topol332.tpr 
> -o area1_332.xvg -n index.ndx
>          0    0.973462     1.61389     2.58735           0
> 
> 2) On all peptides (I chose ALL peptides for surface calculation and ALL
> peptides as the output):
> 
> with 3.3:
> # g_sas -f ../traj1_12_1micro_System_dt100ps.xtc -e 100 -s topol33.tpr 
> -o area33.xvg
>          0     35.3378     40.1608     75.4986           0
> 
> with 3.3.2:
> # g_sas -f ../traj1_12_1micro_System_dt100ps.xtc -e 100 -s topol332.tpr 
> -o area332.xvg
>          0     37.7036     50.8631     88.5667           0
> 
> Am I doing something stupid or is it a bug?
> 
Please search bugzilla for previous problems with g_sas, and if you 
cannot find anything relevant submit a new bugzilla with relevant input etc.

> Thanks,
> 
> Isabella
> 
>  -----------------------------------------------------
>     Dr. Isabella Daidone
>     Computational Molecular Biophysics, IWR
>     University of Heidelberg, Im Neuenheimer Feld 368
>     D-69120 Heidelberg, Germany.
>     Tel.: +49-(0)6221-54-8806, Fax: -8868
>     email: Isabella.Daidone at iwr.uni-heidelberg.de
>     http://matisse.chem.uniroma1.it/isabella/index.html
>  -----------------------------------------------------
> 
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-- 
David van der Spoel, Ph.D.
Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205. Fax: +4618511755.
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se