VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Wed Mar 12 2014 - 12:16:09 CDT

Hi,
  I can't give you a concrete answer, but it would appear that SURF
is failing. I would recommend that you either use the built-in QuickSurf
representation, or the MSMS surface representation instead.

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Wed, Mar 12, 2014 at 03:47:40PM +0530, Shomesankar Bhunia wrote:
> Dear all,
> I had performed a MD simulation on a homology modeled protein using AMBER
> forcefield. The simulation was performed for 2ns. When i loaded the *.dcd
> file in VMD everything is fine but after 9000 frame when i am trying to
> get a SURF graphical representation for the protein I am receiving an
> error
> "ERROR) Cannot read SURF output file: /tmp/vmdsurf.u1000.478.in.tri"
>
> Although the SURF representation is working upto 9000 frames it is not
> working after that. I have reinstalled vmd again for this reason but no
> result. VMD is installed here in ubuntu 12.04 64 bit workstation. Thank
> you in advance.
>
> Regards
> Shome. 

-- 
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/