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: [EMAIL PROTECTED]
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.
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