VMD-L Mailing List

From: Brian Bennion (brian_at_youkai.llnl.gov)
Date: Tue Nov 30 2004 - 16:48:21 CST

I also found that my machine used Starting MSMS with: 'msms -no_area
-socketPort 1360 &'

is there a reason for the difference?
Brian

On Tue, 30 Nov 2004, Brian Bennion wrote:

>
> 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 **
> *****************************************************************
>

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