yes, you want TER lines in between segments
of the chain in your pdb file so that Leap does
not bond them together.
I would suggest using positional restraints (ntr=1)
rather than the ones you mention below.
You will specify the atoms and force constant
in a GROUP input, see the manual for details.
you can use dielc=4 in the input file, but you will
also need to specify the distance-dependent dielectric.
that depends on the AMBER version you are using, which you
did not mention. Check the manual for details.
Carlos
----- Original Message -----
From: Małgorzata Jarończyk
To: amber.scripps.edu
Sent: Thursday, February 12, 2004 4:18 AM
Subject: AMBER: Run calculations for protein in Amber
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
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Received on Thu Feb 12 2004 - 13:53:01 PST
