VMD-L Mailing List

From: hl332_at_drexel.edu
Date: Thu Mar 29 2007 - 18:09:43 CDT

Hi John,
  Thanks for your suggestion and i tried even MSMS but it didnt work either giving this error message:
==========================================
vmd > Info) Starting MSMS with: 'msms -no_area -socketPort 1357 &'
sh: msms: command not found
Info) Waiting for MSMS server ...
Info) Waiting for MSMS server ...
Info) Waiting for MSMS server ...
Info) Waiting for MSMS server ...
ERROR) Could not connect to MSMS server. Please check that the program 'msms' e
xists and is executable, or set the environment variable MSMSSERVER to point to
the correct binary.
Info) Could not compute MSMS surface
Info) Done with MSMS surface.
=========================================

regards
Harish
-------------------------------------------------
Harish Vashisth (Ph.D Candidate)
CAT-361,Chemical & Biological Engg.
Drexel University, Philadelphia, PA
office: 215-895-5823

----- Original Message -----
From: John Stone <johns_at_ks.uiuc.edu>
Date: Thursday, March 29, 2007 5:10 pm
Subject: Re: vmd-l: 'SURF' representation problem

> Hi,
> Have you tried using MSMS instead? MSMS is much newer than Surf
> and is supported by the people at Scripps. Surf hasn't been
> maintainedfor many years now and the version we provide with VMD
> just has various
> bug fixes that we've added ourselves. Give MSMS a try and let us know
> if you still need help.
>
> Cheers,
> John Stone
> vmd_at_ks.uiuc.edu
>
>
> On Thu, Mar 29, 2007 at 05:04:02PM -0400, hl332_at_drexel.edu wrote:
> > Hi,
> > I have been trying to draw my protein and several of its
> residues using surface representation 'SURF' but for some reason it
> displays only a small portion as surf not the whole protein. The
> following commands are executed in vmd console:
> > =================================
> >
> > vmd > Reading 4716 atoms..done
> > Probe radius = 1.400
> > Constructing solvent-accessible surface ..
> > Max edge length = 1.200
> > Malloc of zero or illegal length!!
> > length = 0
> > Malloc of zero or illegal length!!
> > length = 0
> > ...........compute_tri_plane_int(): denom close to zero 0.000000
> > .....................................
> > Total Triangles 255214 Total constraints 228706
> > Max Neighbors per atom 90 Average Neighbors per atom 48.4958
> > Surface construction + writing time 4.94 seconds
> > done
> > Info) This surface is made with SURF from UNC-Chapel Hill. The
> reference is:
> > Info) A. Varshney, F. P. Brooks, W. V. Wright, Linearly Scalable
> Computation> Info) of Smooth Molecular Surfaces, IEEE Comp.
> Graphics and Applications,
> > Info) v. 14 (1994) pp. 19-25.
> > Info) Reading Surf geometry output file...
> > Info) Read Surf output file, processing geometry...
> > Info) Done.
> > ========================================
> >
> > regards
> > Harish
> >
> > -------------------------------------------------
> > Harish Vashisth (Ph.D Candidate)
> > CAT-361,Chemical & Biological Engg.
> > Drexel University, Philadelphia, PA
> > office: 215-895-5823
>
> --
> NIH Resource for Macromolecular Modeling and Bioinformatics
> Beckman Institute for Advanced Science and Technology
> University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
> Email: johns_at_ks.uiuc.edu Phone: 217-244-3349
> WWW: http://www.ks.uiuc.edu/~johns/ Fax: 217-244-6078
>