AMBER Archive (2009)

Subject: [AMBER] Tutorial A3

From: s. Bill (s_bill36_at_yahoo.co.uk)
Date: Sun Jul 19 2009 - 14:33:58 CDT

Dear AMBER
In tutorial A3 (MM-PBSA calcualtion), in section 1 during heating stage, you used two different temperaturre contorls, is this normal? is it enough to define only temperature variation by using :
&wt TYPE='TEMP0', istep1=0, istep2=25000,
  value1=0.1, value2=300.0, /
 &wt TYPE='END' /

Also, in Minimization stage, you minimized solvent only with a constrain on your protein-ligand? why you didn't minimzed protein-ligand complex also?
Why in the production step, he used constant pressure, not constant volume? I would appreciate if you can direct me to one reference dealing with the difference between using constant presssure or volume in the production phase.
Thanks in advance
bill

      
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