From: Peter Freddolino (
Date: Mon Nov 10 2008 - 17:29:24 CST

Autopsf should take care of the split/recombine process automatically,
although you'll want to verify that the results are reasonable. You can
get at it via the command line or GUI (under Modeling).

Edward Lyman wrote:
> 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