VMD-L Mailing List

From: Brian Bennion (brian_at_youkai.llnl.gov)
Date: Tue Nov 30 2004 - 13:15:47 CST

Hmmmm this has got to be a easy problem to solve....

just to confirm, localhost is enabled as 127.0.0.1 ?

# Do not remove the following line, or various programs
# that require network functionality will fail.
127.0.0.1 localhost.localdomain localhost

^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
Is this in your /etc/host file?

how do you turn the firewall off?
/sbin/service iptables stop ?
what is the output after that command?

did you capture the listing for iptables when you enabled port 1357 and
used the vmd options to start msms?

On Mon, 29 Nov 2004, Luis Rosales wrote:

> 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
> >
>
>
>

*****************************************************************
**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 **
*****************************************************************