VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Mon Nov 29 2004 - 00:08:22 CST

Luis, Brian,
  Sorry for the delayed reply, I've been mostly offline for the last 4 days...

MSMS is not listening to the socket when you give it that additional
-if option... In order to test it properly, you need to run it with
the exact options VMD uses. Once you run it that way (giving the port
flag etc) you should be able to telnet to the MSMS port and connect
to it. If you can't connect to it, then that's the source of the problem
that VMD is encountering. Try just using the exact flags that VMD uses,
and telnet to MSMS. Let me know what happens.

  John Stone
  vmd_at_ks.uiuc.edu

On Wed, Nov 24, 2004 at 04:13:44PM -0600, Luis Rosales wrote:
>
> Hi all!
>
> Dear John and Brian:
>
> Thanks for your time,
> Yes, I checked the directory permissions as well as the binary permissions,
> and they are set right for everybody to read/execute (drwxr-xr-x).
> And I have defined localhost on my hosts file... (127.0.0.1
> localhost.localdomain localhost)
>
> So far I had run msms with:
>
> msms -if file.xyzr
> msms -no_area -if 1crn.xyzr
> msms -no_area -socketPort 1357 -if 1crn.xyzr
>
> And every time if indicates a normal termination (this is the output of the
> -no_area -sockerPort 1357 -if):
>
> Arioco_at_ruiz2 15% msms -no_area -socketPort 1357 -if 1crn.xyzr
> MSMS 2.5.5 started on ruiz2.biomedicas.unam.mx
> Copyright M.F. Sanner (1994)
> Compilation flags -O3 -mips3 -xansi -DVERBOSE -DTIMING -DFUNCPROTO -fullwarn
> INPUT 1crn.xyzr 327 spheres 0 collision only, radii 1.400 to 2.000
> PARAM Probe_radius 1.500 density 1.000
> REDUCED SURFACE ...
> RS component 0 identified 211 208 210
> 0 free edge(s) found in component 0
> RS component #faces #edges #free_edges #vertices genus
> 0 430 645 0 210 3.5
> Time Reduced Surface real: 0.04 user: 0.04 sys: 0.00
> ANALYTICAL SOLVENT EXCLUDED SURFACE...
> Component 0
> Time Surface real: 0.01 user: 0.01 sys: 0.00
> Time Singularities real: 0.00 user: 0.00 sys: 0.00
> SES comp. #fac. #edg. #s_edg. #vert. #s_vert. R_h C_h genus
> 0 1304 2616 12 1314 24 0 0 0
> TRIANGULATION...
> Component 0
> component#, vertices, edges, faces, genus, density
> 0 2465 7389 4926 0 0.000
> Time Triangulation real: 0.04 user: 0.04 sys: 0.00
> MSMS terminated normally
> Total Time real: 0.10 user: 0.09 sys: 0.00
>
> -------------------------------------------
>
> So,it appears that the socketport and the no_area options run fine in a
> manual run....
> How can I know if the port is open, so that the communication between vmd
> and msms is happening??
>
> Thanks
>
>
> 

-- 
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