Subject: DCCM in CHARMM

From: Marcin Krol <mykrol<<at>>cyf-kr.edu.pl>
Date: Thu, 29 May 2003 12:00:50 +0200 (METDST)

Hello,

I'd like to calclulate dynamic cross-corelation matrices in CHARMM. So
firstly, I oriented all trajectiory frames on the crystal structre (merge
orient keyword). Then I calculated average structure from the oriented
trajectory and defined times series as fluctuation of all CA atoms (each
CA
atoms represents motions of the whole aminoacid). When I had times series
for all CA atoms I started to calculate

<Q(a)*Q(b)>/sqrt<Q(a)**2>*sqrt<Q(b)**2>

where Q(a) is one time series and Q(b) another.
In principle I should get what I want, but the values I obtain are between
0.8-1.0 no matter what time series are chosen. It looks like motions of
all aminoacids in my protein are highly correlated, which is not very
probable. What can be the reason for it? I have oriented the whole
trajectory on the crystal structure so translations and rotations of the
center of mass should be removed.

Thanks in advance for any suggestions how to obtain correct DCCM in CHARMM

Marcin Krol

Below is the charmm script I use.

1. To remove trans and rot of the center of mass

open crystal struture
read crystal structure

coor copy comp

open input traj files

open output traj files

merge firstu 41 nunit 24 skip 500 outputu 71 nfile 200 sele segid (name of
my protein) end orient sele type CA end

(so I should get a new traj files which contain only protein atoms and
frames are oriented on crystal structure CA atoms)

2. Caluculate DCCM

open crystal structure
read crystal structure

open oriented traj files

coor dyna comp firsu 41 nunit 5

correl maxt 1050 maxseries 433 maxatoms 433 cutnb 2.

set res 1

label enterdccm
	enter a@res fluc r sele resi @res .and. type CA end
 	traj first 41 nunit 5

	incr res by 1
if res lt 433 goto eneterdccm

set res 1

label one
      set res

      label two

  	   mantime a@res fluct a@resn

           incr resn by 1
       if resn lt 433 goto two

       incr res by 1

if res lt 433 goto one

stop
end