VMD-L Mailing List

From: Edward Lyman (edward.lyman_at_gmail.com)
Date: Mon Nov 10 2008 - 16:42:13 CST

Dear all,

I have a pdb and a psf for a membrane system, and I want to build a system
that is twice as big, by shifting the coordinates by the box dimension in y.
shifting the coordinates and writing them to a pdb is simple enough, but I
am trying to find a simple way to generate a combined pdb/psf for the whole,
doubled system. if i try to read the psf and the first pdb, then re-read the
psf and read the second pdb, I get an error "Unable to add (duplicate?)
residue C001:1". but, even if I am able to do so, I think I might have too
many residues per segment.

In the past, I dealt with this by painstakingly splitting the pdb's into
separate segments, renaming segments until I had enough, regenerating the
psf's, and then sticking it all back together with a series of
readpsf/readpdb's, then writing everything. But I think there must be a
cleaner, faster, less annoying way...

Thx,
E