VMD-L Mailing List

From: Andres Morales N (andresmoralesn2_at_hotmail.com)
Date: Thu Sep 17 2009 - 00:03:36 CDT

Dear user:
 
 
I am studing protein conformational substates, I need to get the average structure from clsters of structures, I use the following script to do that:
 
set ref [atomselect top "protein and backbone" frame 0]
set nf [molinfo top get numframes]
set sel [atomselect top "protein and backbone"]
 
#align
 
for {set i 0 } {$i < $nf } { incr i } {
$sel frame $i
$sel move [measure fit $sel $ref]
$sel1 frame $i
 }
 # calculate average structure
 
set sel1 [atomselect top all]
set nf [molinfo top get numframes]
set n [expr $nf - 1]
set newpos [measure avpos $sel1 first 0 last $n step 1]
$sel1 set {x y z} $newpos
$sel1 writepdb "promedio.pdb"
 
 
I need to calculate energy of each average structure. I used NAMDEnergy tool to do it. So the results were not good. For example, I have a cluster of eleven structures (frames) which energy is between -1100 and -1000 kcal/mol (calculated with NAMDEnergy too); but average structure's energy is 15094 kcal/mol. I do know what is wrong. I wait somebody can help me.
 
 
Thanks for your suggestions.
 
 
Andres
 

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