From: lara lara (
Date: Sat Sep 25 2010 - 04:24:09 CDT

Dear NAMD users !

I have followed up the membrane tutorial from namd.

I tried to place the peptide inside the lipid bilayer as being done in the
tutorial. I minimized the whole system to 1000 steps , and tried to
calculate the
interaction energy between the peptide and the membrane by spliting the pdb
as membrane , water and protein .

I can be able to find the energy using the namdenergy.tcl.
but I have a problem when I combine the pdb I am getting the protein and the
monolayer but not the bilayer . The mode of selection that I have done
seems to be wrong. With this I have attached the script which I used
does any one can tell me where I have done the mistake

thanks in advance


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