VMD-L Mailing List

From: Falgun Shah (fhshah_at_olemiss.edu)
Date: Wed Mar 04 2009 - 00:20:59 CST

Now it is working perfectly. Thanks a bunch

On Wed, Mar 4, 2009 at 12:11 AM, John Stone <johns_at_ks.uiuc.edu> wrote:

>
> Hi,
> Set your MSMSSERVER variable to
> /usr/local/bin/MSMS/msms.x86_64Linux2.2.6.1
> If you're still getting something else from within VMD itself, then
> some script or path of yours must be resetting it. You should be able
> to force/override this from within VMD like this:
> set env(MSMSSERVER) /usr/local/bin/MSMS/msms.x86_64Linux2.2.6.1
>
> Cheers,
> John
> - Show quoted text -
>
> On Wed, Mar 04, 2009 at 12:06:27AM -0600, Falgun Shah wrote:
> > Dear john
> >
> > when i executed following command:
> > /usr/local/bin/MSMS/msms.x86_64Linux2.2.6.1 > i received similar message
> as
> > you got
> > MSMS 2.6.1 started on localhost.localdomain
> > Copyright M.F. Sanner (1994)
> > Compilation flags -O2 -DVERBOSE -DTIMING
> > MSMS: No input stream specified
> >
> > when i type in the vmd console:
> >
> > vmd > puts "MSMSSERVER variable:$env(MSMSSERVER)"
> > MSMSSERVER variable:/usr/local/bin/msms
> > vmd > Info) Starting MSMS with: '/usr/local/bin/msms -no_area -socketPort
> > 1357 &'
> > sh: /usr/local/bin/msms: No such file or directory
> > Waiting for MSMS server ...
> > Info) Waiting for MSMS server ...
> > Info) Waiting for MSMS server ...
> > Info) Waiting for MSMS server ...
> > ERROR) Could not connect to MSMS server. Please check that the program
> > '/usr/local/bin/msms' exists and is executable, or set the environment
> > variable MSMSSERVER to point to the correct binary.
> > Info) Could not compute MSMS surface
> > Info) Done with MSMS surface.
> >
> > i have add following line in my /etc/csh.cshrc file
> > setenv MSMSSERVER /usr/local/bin/MSMS/msms.x86_64Linux2.2.6.1
> >
> > i dont know why when i execute command using vmd console it is giving me
> > this message (Starting MSMS with: '/usr/local/bin/msms)
> >
> > please let me know
> >
> > thanks for help
> > On Tue, Mar 3, 2009 at 11:49 PM, John Stone <johns_at_ks.uiuc.edu> wrote:
> >
> > > Hi,
> > > From what you've said below, I can see that the source of your
> > > problem is that you set the MSMSSERVER variable incorrectly. VMD
> > > is expecting the MSMS executable path, not the name of the directory
> > > that contains it. If you have it in an "msms" subdirectory of
> > > /usr/local/bin, then you'd need to set the MSMSSERVER variable
> > > to something like this:
> > > /usr/local/bin/MSMS/msms.X86_64Linux2.2.6.1
> > >
> > > You can check if this variable is being passed on to VMD
> > > by running this command within VMD:
> > > puts "MSMSSERVER variable: $env(MSMSSERVER)"
> > >
> > > You should make sure that the MSMS executable you've specified
> > > actually exists and is runnable, by executing it by hand, e.g.:
> > > /usr/local/bin/MSMS/msms.X86_64Linux2.2.6.1
> > >
> > > You should see output akin to this (when I run it on my system):
> > > johns_at_casablanca.ks.uiuc.edu{26} /usr/local/bin/msms
> > > MSMS 2.5.5 started on casablanca.ks.uiuc.edu
> > > Copyright M.F. Sanner (1994)
> > > Compilation flags -O3 -mips3 -xansi -DVERBOSE -DTIMING -DFUNCPROTO
> > > -fullwarn
> > > MSMS: No input stream specified
> > >
> > > Cheers,
> > > John
> > >
> > > On Tue, Mar 03, 2009 at 11:31:24PM -0600, Falgun Shah wrote:
> > > > Dear John
> > > >
> > > > when i executed command /usr/local/bin/msms/pdb_to_xyzr 1crn.pdb >
> > > 1crn.xyzr
> > > > it worked fine. and i got 1crn.xyzr file.
> > > >
> > > > so it is working in that way. It would be wonderful if i can run it
> > > through
> > > > vmd as i need to do select only few residues for surface generation
> as
> > > well
> > > > color them differently.
> > > >
> > > > Thanks. i will be waiting for your reply
> > > >
> > > > On Tue, Mar 3, 2009 at 11:21 PM, John Stone <johns_at_ks.uiuc.edu>
> wrote:
> > > >
> > > > > Hi,
> > > > > What happens if you execute /usr/local/bin/msms manually? Do you
> > > > > get an error, or does it run succesfully?
> > > > >
> > > > > Cheers,
> > > > > John Stone
> > > > > - Show quoted text -
> > > > >
> > > > > On Tue, Mar 03, 2009 at 10:36:20PM -0600, Falgun Shah wrote:
> > > > > > Dea john
> > > > > >
> > > > > > I am trying to generate surface using MSMS. It is giving me
> following
> > > > > error:
> > > > > > Waiting for MSMS server ...
> > > > > >
> > > > > > puts $env(MSMSSERVER
> > > > > > /usr/local/bin/msms
> > > > > > vmd > Info) Starting MSMS with: '/usr/local/bin/msms -no_area
> > > -socketPort
> > > > > > 1358 &'
> > > > > > sh: /usr/local/bin/msms: No such file or directory
> > > > > > Info) Waiting for MSMS server ...
> > > > > > Info) Waiting for MSMS server ...
> > > > > > Info) Waiting for MSMS server ...
> > > > > > ERROR) Could not connect to MSMS server. Please check that the
> > > program
> > > > > > '/usr/local/bin/msms' exists and is executable, or set the
> > > environment
> > > > > > variable MSMSSERVER to point to the correct binary.
> > > > > > Info) Could not compute MSMS surface
> > > > > > Info) Done with MSMS surface.
> > > > > >
> > > > > > I have gone through the VMD mailing list. Similar error is
> reported.
> > > But
> > > > > > still i was unable to find what is going wrong. What i have done
> is
> > > as
> > > > > > follows: i have downloaded msms from here:
> > > > > > http://www.scripps.edu/~sanner/html/msms_home.html>
> <http://www.scripps.edu/%7Esanner/html/msms_home.html>
> > > <http://www.scripps.edu/%7Esanner/html/msms_home.html>
> > > > > >
> > > > > > Downloaded file: msms.x86_64Linux2.2.6.1 i tried to convert
> example
> > > file
> > > > > > 1crn.pdb to 1crn.xyzr using pdb_to_xyzr script. however it gave
> me an
> > > > > error
> > > > > > message: ./pdb_to_xyzrn: line 102: nawk: command not found
> > > > > >
> > > > > > so i modified the script and replace awk with gawk but it did not
> do
> > > > > > anything.
> > > > > >
> > > > > > then i tried to copy all the downloaded files MSMS to
> > > usr/loca/bin/MSMS.
> > > > > > vmd is also installed here: alias
> vmd='/home/Amber9.0/vmd-1.8.6/vmd
> > > > > > my local host is also defined.
> > > > > >
> > > > > > In my /etc/csh.cshrc file i have included: setenv MSMSSERVER
> > > > > > /usr/local/bin/MSMS/msms.X86_64Linux2.2.6.1
> > > > > >
> > > > > > i am not able to figure out what was wrong. please let me know if
> you
> > > > > need
> > > > > > some more information.
> > > > > >
> > > > > >
> > > > > >
> > > > > >
> > > > > > On Tue, Mar 3, 2009 at 2:51 PM, John Stone <johns_at_ks.uiuc.edu>
> > > wrote:
> > > > > >
> > > > > > >
> > > > > > > Hi,
> > > > > > > I'd suggest using MSMS for your surface representation, as it
> > > gives
> > > > > > > nice looking surfaces. You can draw springs and other
> graphical
> > > > > objects
> > > > > > > using the "draw" or "graphics" commands in VMD. There are
> various
> > > > > example
> > > > > > > scripts for drawing arrows etc in the VMD/CPMD tutorial here:
> > > > > > >
> > > > > > >
> > > > >
> > >
> http://www.theochem.ruhr-uni-bochum.de/~axel.kohlmeyer/cpmd-vmd/part7.html#chap9_sect1>
> <
> http://www.theochem.ruhr-uni-bochum.de/%7Eaxel.kohlmeyer/cpmd-vmd/part7.html#chap9_sect1
> >
> > > <
> > >
> http://www.theochem.ruhr-uni-bochum.de/%7Eaxel.kohlmeyer/cpmd-vmd/part7.html#chap9_sect1
> > > >
> > > > > <
> > > > >
> > >
> http://www.theochem.ruhr-uni-bochum.de/%7Eaxel.kohlmeyer/cpmd-vmd/part7.html#chap9_sect1
> > > > > >
> > > > > - Show quoted text -
> > > > > > >
> > > > > > > There's an old spring drawing script here:
> > > > > > >
> > > http://www.ks.uiuc.edu/Research/vmd/script_library/scripts/spring/
> > > > > > >
> > > > > > > Cheers,
> > > > > > > John Stone
> > > > > > > vmd_at_ks.uiuc.edu
> > > > > > >
> > > > > > > On Sun, Mar 01, 2009 at 03:23:12PM -0600, Falgun Shah wrote:
> > > > > > > > Dear Vmd users
> > > > > > > >
> > > > > > > > I am doing constant velocity smd simulation of the protein of
> my
> > > > > > > interest. I
> > > > > > > > want to generate final image of the protein in surface
> > > representation
> > > > > > > along
> > > > > > > > with virtual spring showing 3 direction of egress for my
> ligand.
> > > > > Please
> > > > > > > let
> > > > > > > > me know the best way to generate molecular surface of protein
> > > binding
> > > > > > > site
> > > > > > > > and how to insert spring between COM of the smd atoms and the
> > > > > calculated
> > > > > > > > direction. Your recommendations are most welcome. Thanks in
> > > advance.
> > > > > > > > --
> > > > > > > > Falgun H shah
> > > > > > > > PhD candidate (3rd year)
> > > > > > > > Department of Medicinal Chemistry
> > > > > > > > 2028, Natural Product Center
> > > > > > > > University of Mississippi
> > > > > > > >
> > > > > > > > Ph No: 6629151286(O)
> > > > > > > > 662 801 5667(M)
> > > > > > > > email: fhshah_at_olemiss.edu
> > > > > > >
> > > > > > > --
> > > > > > > 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/>
> <http://www.ks.uiuc.edu/%7Ejohns/>
> > > <http://www.ks.uiuc.edu/%7Ejohns/><
> > > > > http://www.ks.uiuc.edu/%7Ejohns/>
> > > > > > > Fax: 217-244-6078
> > > > > > >
> > > > > >
> > > > > >
> > > > > >
> > > > > > --
> > > > > > Falgun H shah
> > > > > > PhD candidate (3rd year)
> > > > > > Department of Medicinal Chemistry
> > > > > > 2028, Natural Product Center
> > > > > > University of Mississippi
> > > > > >
> > > > > > Ph No: 6629151286(O)
> > > > > > 662 801 5667(M)
> > > > > > email: fhshah_at_olemiss.edu
> > > > >
> > > > > --
> > > > > - Show quoted text -
> > > > > 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/>
> <http://www.ks.uiuc.edu/%7Ejohns/><
> > > http://www.ks.uiuc.edu/%7Ejohns/>
> > > > > Fax: 217-244-6078
> > > > >
> > > >
> > > >
> > > >
> > > > --
> > > > Falgun H shah
> > > > PhD candidate (3rd year)
> > > > Department of Medicinal Chemistry
> > > > 2028, Natural Product Center
> > > > University of Mississippi
> > > >
> > > > Ph No: 6629151286(O)
> > > > 662 801 5667(M)
> > > > email: fhshah_at_olemiss.edu
> > >
> > > --
> > > 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/><
> http://www.ks.uiuc.edu/%7Ejohns/>
> > > Fax: 217-244-6078
> > >
> >
> >
> >
> > --
> > Falgun H shah
> > PhD candidate (3rd year)
> > Department of Medicinal Chemistry
> > 2028, Natural Product Center
> > University of Mississippi
> >
> > Ph No: 6629151286(O)
> > 662 801 5667(M)
> > email: fhshah_at_olemiss.edu
>
> --
> 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/ <http://www.ks.uiuc.edu/%7Ejohns/>
> Fax: 217-244-6078
> 

-- 
Falgun H shah
PhD candidate (3rd year)
Department of Medicinal Chemistry
2028, Natural Product Center
University of Mississippi
Ph No: 6629151286(O)
          662 801 5667(M)
email: fhshah_at_olemiss.edu