Subject: Summary: MD trajectory analysis

From: [email-masked] (Leif Olson)
Date: Wed, 1 Feb 95 18:28:12 -0800

Netters:

Here is a summary of the responses I got for a request for molecular
dynamics trajectory analysis software.  I was interested in a program
which can do the same things as "Curves, Dials, and Windows", 
part of the "Molecular Dynamics Analysis Toolchest" of Ravishanker and
Beveridge at Wesleyan University.  The MD Toolchest is between versions
and so is (unfortunately) temporarily unavailable. 

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Hi Leif,

I don't know exactly what you are looking for and on which platform
you plan to run the software but I have a program named SCARECROW
which could be helpful.

If you are interested you can have a look at it either through
WWW or ftp.

WWW URL: http://www.csc.fi/lul/chem/scarecrow/jmg_scare.html

or

Anonymous ftp from nic.funet.fi in directory /pub/sci/chem/scarecrow

Regards,

-leif laaksonen
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Leif Laaksonen                     |
Center for Scientific Computing    | Phone:      358 0 4572378
P.O. Box 405                       | Mobile:     358 400425203
FIN-02101 Espoo                    | Telefax:    358 0 4572302
FINLAND                            | Mail:  [email-masked]
---------URL: http://laaksonen.csc.fi/leif.laaksonen.html----------

              I dreamed that, as I wandered by the way,
              Bare winter suddenly was changed to spring.

                                    P.B. Shelley
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Dear Dr. Olson
        You could try to run NUPARM, after separating all the
coordinate files in separate pdb files, naming them as file#.pdb.
The program NUPARM is available in Brookhaven Protein Data Bank,
however I am sending you separately a latest version of it along 
with a sample c-shell script to run NUPARM for a number of coordinate 
files.  This script would create structure data for all the coordinate 
files in different files, named after the coordinate file.  You may 
use unix "grep" and "cut" commands later to pick out the selected 
structural parameters from the name#.prm files.  
        Best wishes and please feel free to call me if you have any 
questions/problems in running this program.

                                Dhananjay Bhattacharyya

[email-masked]

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        I have an analysis program which you can script to
run at the end of whatever cycles, it doesn't output like dials
and window but it does give all complementary parameters and
Cartesian and helical parameters from the local view between
neighboring bases and basepairs. I had articles in last years JMB and
JBSD.
        Let me know if a single run program with comparable parameters
is what you can use.
                        Marla Babcock

[email-masked]

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My impression is that Curves/dials/windows is for analyzing
trajectories generated w/ dynamics programs, rather than
being a dynamics program per se. See our Web page for a reference
to SCARECROW, another analysis package.

See: http://www.amber.ucsf.edu/amber/amber.html

Bill Ross

[email-masked]

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Dr Olson:

I read your posting on CCL.  Our lab along with Dr. David Doherty has
developed a program called MOLSIM.  It may help resolve your problem.
Following is an excerpt from its manual,

"The mda module

The mda option of Molsim is an interactive MD analysis facility, which
operates on either the trajectory files output by mdsim or the energy files
output by mdsim (choose "none" upon starting up mda). Some of the types of
analysis provided by mda include: saving of a particular frame of the
trajectory file to a molecule file; bond length, bond angle, torsion angle,
or atom-atom distance monitoring and averaging over the course of the
trajectory; calculation of thermodynamic properties (assuming a canonical
ensemble and an equilibrium trajectory) from the energy files output by
mdsim (choose "none" when mda asks for a trajectory file definition);
calculation of certain polymer properties from the trajectory; and more.
mda can act upon several consecutive trajectories, treating them as one
continous trajectory. This is accomplished by creating a text file which
contains the name of each of the trajectory files on a separate line, then
choosing "multiple" when mda starts up."

MOLSIM software is a commercial program.  If you wish furthur information,
please let me know.  You can also directly contact Dr.
Doherty([email-masked]) or Dr. Hopfinger([email-masked]).

Good Luck,

Hitesh C.Patel

Laboratory of Molecular Modeling and Design
College of Pharmacy
Univ. of Illinois at Chicago
833 S. Wood St., m/c 781, #539
Chicago, IL 60612

312 996 6002
312 996 6004

fax:    312 996 7107

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-We are looking at some of these packages now.  We have about 13,000 DNA
molecular dynamics structures in CHARMm DCD files, so we need to reduce
the data to digestible chunks for understanding and publication.  So far,
the easiest way to this still appears to be Curves, Dials and Windows,
but some of the other programs have some very intriguing features that 
we can probably use for future analyses of biomolecular structures.

Thanks very much to the respondents!

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Leif P. Olson, Ph.D.		|	phone: 805-893-2234
(Bruice Lab)			|
UC Santa Barbara Chemistry Dept.|	[email-masked]

"Yes, it does rain in Southern California"
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