VMD-L Mailing List

From: Ting Wang (twang_at_ucdavis.edu)
Date: Thu May 11 2006 - 15:09:07 CDT

Hi,

I have a problem to generate a psf for POPC lipid molecules by using psfgen.

My membrane is a combination of two smaller pieces generated by using
"membrane -l popc .. " in VMD (because VMD generates serious clash larger
membrane, I had to use this way to get a large piece of membrane ). But to
use the script combine.tcl to insert my GPCR protein into the membrane, I
need the psf file of the membrane. I was using the following commands, a
psf file was indeed generated but with lots of warning and a wrong total
atom number.

> mol new membrane.pdb
> package require psfgen
> topology top_all27_prot_lipid.inp
> segment U {pdb membrane.pdb}
> coordpdb membrane.pdb U
> guesscoord
>writepdb membrane0.pdb
>writepsf membrane0.psf

Can anybody help? Thanks a lot!

Ting