[gmx-users] g_sas => calculate the SASA for each residues ?

[Chih-Ying Lin]

Hi
How can I calculate the SASA for each residue ?
>From Manual => "The program will ask for a group for the surface calculation
and a group for the output."



When I issue the command => g_sas -f  abc.gro   -s   abc.tpr  -n
Residue1.ndx -o SASA.xvg
=> Gromacs will pick Residue1.ndx as both a group for the surface
calculation and a group for the output.



When I issue the command => g_sas -f  abc.gro   -s   abc.tpr  -n
Residue1.ndx -n protein.ndx -o SASA.xvg
=> Gromacs will show => Fatal error:Double command line argument -n



I want protein.ndx as a group for the surface calculation and Residue1.ndx
as a group for the output.
How to do fix the problem ?

Thank you
Lin










Group     0 (      System) has 20659 elements
Group     1 (     Protein) has  1321 elements
Group     2 (   Protein-H) has  1001 elements
Group     3 (     C-alpha) has   129 elements
Group     4 (    Backbone) has   387 elements
Group     5 (   MainChain) has   517 elements
Group     6 (MainChain+Cb) has   634 elements
Group     7 ( MainChain+H) has   646 elements
Group     8 (   SideChain) has   675 elements
Group     9 ( SideChain-H) has   484 elements
Group    10 ( Prot-Masses) has  1321 elements
Group    11 ( Non-Protein) has 19338 elements
Group    12 (         azo) has   330 elements
Group    13 (         SOL) has 19008 elements
Group    14 (       Other) has 19338 elements
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