There is a module called "average_structure" in a software package
"Molecular Dynamics ToolChest(MDTC)". This module can do strcutre averages
on a subset of the molecule as well as superpositions. MDTC consists of
dozens of modules for the analysis part of MD simulation with Amber, Charmm
and Gromos etc. Interested users could have a look at
http://ludwig.chem.wesleyan.edu/~wwang/mdtool and try out with its
pre-release version.
-----Original Message-----
From: Carlos Simmerling [mailto:carlos.simmerling_at_sunysb.edu]
Sent: Thursday, March 29, 2001 12:56 PM
To: amber_at_cgl.ucsf.edu
Subject: Re: Average structure
What I usually do when I want an "average" structure is
to use MOIL-View to do a cluster anaalysis of the trajectory,
then have it save the most representative structure. This
is the one with the lowest average RMSD to all of the
others in the cluster. It makes it a physical structure that is
a good model for the ensemble that makes up that family.
MOIL-View does this automatically, other programs may do it too.
Carlos
David Konerding wrote:
> "Guanglei Cui" writes:
>
>> I think MoilView by Carlos Simmerling and ptraj by Tom Cheatham both can
>> generate average structures from dynamics. However, the averaged
structure
>> can be distorted, especially when there's large conformational change
such
>> as terminal base pair opening. I've seen the ring of one terminal base
>> shrinked significantly. Minimization doesn't help to correct this as far
as
>> I know. Good luck!
>
>
> Right, imagine the case of a sugar pucker which repuckers between C2' endo
and
> C3' endo. If the populations are 50% each, and you average them, you
> end up with a planar sugar pucker which is physically impossible.
Minimization
> with pop the pucker down to the local minimum, but I doubt that's
particularly relevant
> or useful.
>
> As for averaging, I usually use carnal or my own code. Once you've RMS
aligned the
> structures to a common structure, you can just do a vector additon of the
coordinate
> sets and then divide by scalar number of frames. Or, pre-divide and then
sum.
--
===================================================================
Carlos L. Simmerling, Ph.D.
Assistant Professor Phone: (631) 632-1336
Department of Chemistry Fax: (631) 632-7960
SUNY at Stony Brook Web: http://comp.chem.sunysb.edu/carlos
Stony Brook, NY 11794-3400 E-mail: carlos.simmerling_at_sunysb.edu
===================================================================
Received on Thu Mar 29 2001 - 11:51:05 PST
