VMD-L Mailing List

From: Ralph Jimenez (rjimenez_at_jila.colorado.edu)
Date: Thu May 10 2007 - 20:38:00 CDT

Hiroki,
  Thank you for your e-mail. The path was indeed the problem. When I put the
msms executable into /usr/bin, everything works fine.
   Best wishes,
Ralph

Morizono, Hiroki wrote:
> Ralph,
>
> msms:command not found
> sounds like you don't have paths pointing to msms set correctly.
>
> Having watched this thread fail to die,
> I think you'll find O'Reilly's Unix CD Bookshelf very useful.
> You can install it in ~/Sites or /Library/Webserver/Documents
> and read it at your leisure. It's a collection of half a dozen
> books on one disk. The ksh book will mostly apply to bash.
> I happen to be a happy user of their books,
> and not connected in any way to O'Reilly.
>
> Change directories to where the msms binary is
> and try
> $ ./msms
> and you should get a different error message like
> No input specified
> If you don't, then there are other problems with the way you unpacked
> and installed
> msms, and that needs to be fixed first.
>
> You may need to create an environmental variable
> MSMSSERVER pointing to your msms executable (this is what I have on my
> mac) or perhaps place msms on a standard
> path location.
> (I'm still using vmd 1.85--I have downloaded 1.86, but not gotten around
> to installing it yet)
>
> Since you had to create the .bashrc file, it means you probably only
> have the default set of paths
> ie /bin /usr/bin /usr/sbin
> A good place to add to your $PATH is /usr/local/bin
> and to stick your own unix programs and commands (ie msms and others) in
> a directory called /usr/local/bin
>
> after you source .profile or .bashrc
> you should be able to type in the Terminal
> $ which msms
> and if it returns
> /usr/local/bin/msms
> you ought to be good to go.
>
>
> Hiroki
>
>
>
> -----Original Message-----
> From: owner-vmd-l_at_ks.uiuc.edu on behalf of Ralph Jimenez
> Sent: Tue 5/8/2007 11:38 PM
> To: Dan Wright
> Cc: John Stone; vmd-l_at_ks.uiuc.edu
> Subject: Re: vmd-l: installing MSMS on OS X 10.4.9 (Intel)
>
> Gentlemen,
> Thanks for your help. I opened a bash shell window where I created the
> .bashrc
> file and linked it to .bash_profile as suggested by Dan. I then opened
> VMD and
> ran the puts "$env(VMDMSMSUSEFILE)" command at the VMD prompt, to which it
> returned "1", which I guess means the variable is found.
> However, when I select the msms drawing method from the graphical
> representations, it doesn't work, and gives me this error:
>
> sh: line 1: msms: command not found
> ERROR) Cannot read MSMS facet file: /tmp/vmdmsms.u501.534.face
> Info) Could not compute MSMS surface
> Info) Done with MSMS surface.
> RCNE SendEventToEventTarget (suom Moved ) failed, -50
>
> I verified that msms is in the directory where VMD starts.
> Ralph
>
>
>
>
> 

-- 
-----------------------------------------------
Ralph Jimenez, Ph.D.
JILA/NIST and Department of Chemistry & Biochemistry
440 UCB
University of Colorado, Boulder
Boulder, CO 80309-0440
Tel: (303) 492-8439
FAX: (303) 492-5235
http://jilawww.colorado.edu/JimenezLab/