AMBER Archive (2004)

Subject: AMBER: Run calculations for protein in Amber

From: Małgorzata Jarończyk (warka_at_il.waw.pl)
Date: Thu Feb 12 2004 - 03:18:20 CST

I have started md calculation for protein with restrains. If I have the model of protein without loops should I use'TER' after each helix when I prepare the coordinate file in the xleap for the amber calculations?

And I want to ask you about the line in the input file:

&wt type='REST', istep1= , istep2= ,value1=1.0, value2=1.0, &end

should it be always when I run the calculations with restrains? Does it give information about force of restraints during calculations?

I want to use distance dependent dielectric function 4r as for biological systems, which commands should I put into input file?

Malgorzata Jaronczyk
National Institute of Public Health
Warsaw, Poland

-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu