VMD-L Mailing List

From: Luis Rosales (ludwig_at_biomedicas.unam.mx)
Date: Mon Nov 29 2004 - 18:38:55 CST

Hi all,

I just checked msms with the exact options used by vmd, and from wahat I
could see, msms is having touble with the -socketPort option. I am able to
run msms with just the -no_area option (it just complains about the lack of
a input file), however, when I use the socketport option (alone or with the
-no_area), it crashes and generates a core dump file.

I tried the following (using the same options that vmd uses):

turning off the firewall,
enabling the port 1357,
Using a different port,

With no difference on the outcome...

Thanks,

Luis

> -----Mensaje original-----
> De: owner-vmd-l_at_ks.uiuc.edu [mailto:owner-vmd-l_at_ks.uiuc.edu]
> En nombre de John Stone
> Enviado el: Lunes, 29 de Noviembre de 2004 00:08
> Para: Luis Rosales
> CC: vmd-l_at_ks.uiuc.edu; 'Brian Bennion'
> Asunto: Re: vmd-l: MSMS variable
>
>
> 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
>