how to generate psf for membrane+protein

From: Jiao, Dian NMN (-EXP) (dnjiao_at_sandia.gov)
Date: Mon Apr 09 2012 - 18:16:59 CDT

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Hi,

I've been running simulations for a channel protein which is embeded in a lipid bilayer and solvated in water. Now I also want to run another set of simulations for a mutant with a couple of residue mutations on the protein. I performed the mutations with pymol on the pdb file for the whole system (protein+membrane+solvent). But when I was trying to generate psf file using VMD autopsf, it turned out the membrane and solvent atoms are missing in the new pdb/psf file. Is there way to keep the membrane while creating psf? Thanks.

Dian

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