VMD-L Mailing List

From: Morizono, Hiroki (HMorizono_at_cnmcresearch.org)
Date: Wed May 09 2007 - 08:56:52 CDT

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