VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Tue Mar 03 2009 - 23:49:42 CST

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>
> > >
> > > 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
> > >
> > - 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/>
> > > > 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/>
> > 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/      Fax: 217-244-6078