AMBER Archive (2004)

Subject: Re: AMBER: Run calculations for protein in Amber

From: Carlos Simmerling (carlos_at_csb.sunysb.edu)
Date: Thu Feb 12 2004 - 07:18:32 CST

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_at_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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