On 9/2/12 2:10 PM, venkatesh s wrote:
Dear Sir / Madam,
I want run Solvent accessible surface area in
gromacs,i aware about g_sas is there but for selecting group little bit
confusing
Reading frame 0 time 0.000 Select a group for calculation of
surface and a group for output:
Group 0 ( System) has 210538 elements
Group 1 ( Protein) has 1517 elements
Group 2 ( Protein-H) has 1199 elements
Group 3 ( C-alpha) has 158 elements
Group 4 ( Backbone) has 474 elements
Group 5 ( MainChain) has 633 elements
Group 6 ( MainChain+Cb) has 779 elements
Group 7 ( MainChain+H) has 789 elements
Group 8 ( SideChain) has 728 elements
Group 9 ( SideChain-H) has 566 elements
Group 10 ( Prot-Masses) has 1517 elements
Group 11 ( non-Protein) has 209021 elements
Group 12 ( Other) has 6200 elements
Group 13 ( DPPC) has 6200 elements
Group 14 ( CL) has 21 elements
Group 15 ( Water) has 202800 elements
Group 16 ( SOL) has 202800 elements
Group 17 ( non-Water) has 7738 elements
Group 18 ( Ion) has 21 elements
Group 19 ( DPPC) has 6200 elements
Group 20 ( CL) has 21 elements
Group 21 ( Water_and_ions) has 202821 elements
Select a group: 1
Selected 1: 'Protein'
*Select a group: ? (Which I want Select)*
kindly provide answers
From g_sas -h:
"The program will ask for a group for the surface calculation and a group for
the output. The calculation group should always consists of all the non-solvent
atoms in the system. The output group can be the whole or part of the
calculation group."
-Justin
--
========================================
Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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