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

[Justin A. Lemkul]

Chih-Ying Lin wrote:
> 
> 
> 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 ?
> 

You need both groups in the same index file.  As noted by the fatal error, you 
cannot supply two index files separately.

-Justin

> Thank you
> Lin
> 
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> 
> 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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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
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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