I need help with this

From: Richard Wood (rwoodphd_at_yahoo.com)
Date: Wed Feb 09 2011 - 13:01:25 CST

Hi all,

I'm trying to set up a system where I have a lipid bilayer and I want to
"attach" a small molecule to the surface so I can run dynamics.

I have generated the bilayer using VMD and I have built the small molecule and
have parameters and a topology for it. The problem I am having is in generating
the psf for the total system.

I have the *.pdb and *.psf for the bilayer and I can run that in namd; in fact,
I am minimizing it now as a test. However, when I try to generate a psf file,
because the bilayer is numbered "funny", some residues have the same number and
don't get converted to the new file. If I try to renumber everything by hand,
then it won't minimize (it gets to about 27 steps and then I get "weird numbers"
like -1.

I'm wondering if anyone has encountered this before and what the workaround is.



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