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
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
--
========================================
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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