VMD-L Mailing List

From: Andres Morales N (andresmoralesn2_at_hotmail.com)
Date: Wed Sep 16 2009 - 14:27:23 CDT

Dear user:
 
 
I am studing protein conformational substates, I need to get the average strture form 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. I wait somedoy can help me.

 

 

Thanks for your suggestions.

 

 

Andres

 

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