nitu sharma wrote:
Dear all
I am on the final step of MD simulation of
membrane protein . the final mdrun has successfully completed after
that I have filtered the water from the system .next step is to convert
it in final pdb to view it in pymol for this I am using "trjconv" in
this step I have to select a group from this option-
Group 0 ( System) has 419010 elements
Group 1 ( Protein) has 9902 elements
Group 2 ( Protein-H) has 7778 elements
Group 3 ( C-alpha) has 1000 elements
Group 4 ( Backbone) has 3000 elements
Group 5 ( MainChain) has 4000 elements
Group 6 (MainChain+Cb) has 4922 elements
Group 7 ( MainChain+H) has 4961 elements
Group 8 ( SideChain) has 4941 elements
Group 9 ( SideChain-H) has 3778 elements
Group 10 ( Prot-Masses) has 9902 elements
Group 11 ( Non-Protein) has 409108 elements
Group 12 ( DMPC) has 5520 elements
Group 13 ( SOL) has 403578 elements
Group 14 ( NA+) has 10 elements
Group 15 ( Other) has 409108 elements
Select a group:
for protein with lipid bilayer which group is suitable can anyone
suggest me?
It seems to me that you haven't actually "filtered water", but that you
may wish to create a suitable index group. See
http://oldwiki.gromacs.org/index.php/Index_File
Mark
Becoz a/c to my opinion in group 0 there may be water also but I want to
remove water .
so please if anyone have idea about this please suggest me .
thanks a lot.
Nitu Sharma.
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