VMD-L Mailing List

From: Peter Freddolino (petefred_at_ks.uiuc.edu)
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).
Best,
Peter

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
>