VMD-L Mailing List

From: Falgun Shah (fhshah_at_olemiss.edu)
Date: Wed Mar 04 2009 - 00:06:27 CST

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>
> > > >
> > > > 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
> > > >
> > > - 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/>
> > > > > 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/ <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