VMD-L Mailing List

From: JC Gumbart (gumbart_at_ks.uiuc.edu)
Date: Mon Sep 19 2011 - 01:56:14 CDT

I didn't test this, but it should be more or less correct.

package require psfgen

topology top_all27_prot.inp
#(something like this)

readpsf ubq.psf
coordpdb ubq.pdb
# whatever your file names are - note that this can be the whole system including water, etc.

for {set i 1} {$i <= 35} {incr i} {
  delatom U $i
#where U is the segname
}

delatom U 76
# ubiquitin has 76 residues, right?

patch NTER U:36
patch CTER U:75
# assuming you want default termini

guesscoord
regenerate angles dihedrals

writepsf ubq-frag.psf
writepdb ubq-frag.pdb

On Sep 18, 2011, at 11:43 AM, Trung Nguyen Duc wrote:

> Dear all,
> I am now working with the protein ubiquitin. My project focuses on the molecule dynamics at high temperature and I need to stimulate a fragment ( residues 36-75) of this one. So, my question is that could VMD can create a fragment of the given protein? And could you please suggest me the way to create a fragment?
> Thank you very much!