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 - 09:53:00 PST
