VMD-L Mailing List

From: Bharat Kumar (bharat.stanam_at_gmail.com)
Date: Wed Dec 29 2010 - 09:55:21 CST

Hi

I minimized a protein embedded in a 100 X 100 POPC lipid layer with MOE. I
want to also minimize the output pdb of MOE using NAMD. But the MOE
minimized PDB has some broken lipids. When I generate PSF using psfgen i
find some weird bond formations. And also the autopsf-generated PSF and PDB
files are half less dense than the input PDB. Half lipids go missing. So I
am trying to remove all the lipid fragments that are flying apart. I am
doing this manually.

Does VMD contain any tool to fix these sort of files? I think I can fix the
weird bonds by removing the fragments. But I cannot understand the reduction
in density of lipid layer. Can you please explain why there is a reduction
in lipids after psf?

Thanks,
Bharat.