VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Tue Jan 14 2014 - 09:45:43 CST

Hi,
  I'm afraid that much more information would be needed in order
to help you. Does your DCD file have correct PBC unit cell dimensions
in it? It pays to double check all of that when you get an unexpected
result. Has the trajectory file been post-processed by any scripts
or other programs since it was generated?

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Fri, Jan 10, 2014 at 10:01:22AM -0800, Ramin Ekhteiari wrote:
> Hi dears,
> I did a MD run, that include dimer protein (HIV), when I 'm loading the
> DCD file into VMD, trying to keep the protein at the centre of the box by
> using these commands: *pbc wrap -centersel "protein" -center com -compound
> residue -all *
> But at the result I got lines between 2 monomer of proteins and not
> centred.
> I would greatly appreciate for any advice...
> Cheers 

-- 
NIH Center for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
http://www.ks.uiuc.edu/~johns/           Phone: 217-244-3349
http://www.ks.uiuc.edu/Research/vmd/