From: doty alexiou (doty_alexiou_at_hotmail.com)
Date: Thu Nov 26 2009 - 15:40:09 CST
I am trying to make a CG simulation of a protein in order to study protein-protein interaction. I read at : Four-scale description of membrane sculpting by Ba-domains(Anton Arkhipov,Ying Yin, Klaus Schulten), that i have to add harmonic contsraints to preserve the tertiary structure. I guess that I have to add the harmonic constraints parameters in the configuration file. But how should look like a consref file and a conskfile? Can i find an example of this kind of files?
Shall i also specify a certain direction (X,Y,Z)?
In order to chose the right constant i guess i should monitore the dynamics of the protein..but how exactly?I dont have a membrane,so should i let the CGprotein alone ''running'' using different constants and then chose which is closer to the all-atom ''running''?
Thank you in advance!
_________________________________________________________________
Windows Live Hotmail: Your friends can get your Facebook updates, right from HotmailŪ.
http://www.microsoft.com/middleeast/windows/windowslive/see-it-in-action/social-network-basics.aspx?ocid=PID23461::T:WLMTAGL:ON:WL:en-xm:SI_SB_4:092009
This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 15:53:32 CST