From: Brian Bennion (brian_at_youkai.llnl.gov)
Date: Wed Nov 24 2004 - 16:23:55 CST

Something crazy, but do you have a very restrictive firewall running on
your machine?

Brian

On Wed, 24 Nov 2004, 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
>
>
>
>

*****************************************************************
**Brian Bennion, Ph.D. **
**Computational and Systems Biology Division **
**Biology and Biotechnology Research Program **
**Lawrence Livermore National Laboratory **
**P.O. Box 808, L-448 bennion1_at_llnl.gov **
**7000 East Avenue phone: (925) 422-5722 **
**Livermore, CA 94550 fax: (925) 424-6605 **
*****************************************************************