[gmx-users] g_sas doubt -reg

[Justin Lemkul]

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

-- 
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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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