AMBER Archive (2007)

Subject: AMBER: Hbonds

From: mbrut_at_laas.fr
Date: Wed Jun 13 2007 - 07:54:52 CDT

I try to minimize a DNA-dodecamer with SANDER in implicit solvent,
and then to make a normal mode analysis with NMODE.

 When I look at my structure at the end of the minimization, there are
 no more H-bonds between the bases...
 Is there a problem in my input files ? Maybe I should better work in
 explicit solvent, but it seems very difficult to minimize with the
 precision required to get the good frequencies....
 I am a new user and I'm not sure of the procedure...

 12-mer minimisation GB model
  &cntrl
   imin = 1,
   ntmin = 2,
   maxcyc = 1000000,
   drms = 0.0001,
   ntb = 0,
   igb = 1,
   dielc = 4,
   cut = 12,
  &end
  &ewald
   eedmeth= 5
  &end

  NMA
  &data
   ntrun = 1,
   drms = 0.0001,
   maxcyc = 100,
   scee = 1.2,
   dielc = 4,
   cut = 12
  &end
  &ewald
   eedmeth= 5
  &end

  Please help me !

  Thank you,

  Marie Brut

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