AMBER Archive (2007)

Subject: AMBER: [Fwd: Tr: H bonds]

From: Guillaume Renvez (grenvez_at_laas.fr)
Date: Wed Jun 13 2007 - 07:37:20 CDT

attached mail follows:

Je n'arrive pas a envoyer de mails a l'exterieur...
Tu peux l'envoyer a AMBER pour moi s'il te plait?

Merci,
Marie

             
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attached mail follows:

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 = 1,
  drms = 0.0001,
  ntb = 0,
  igb = 1,
  dielc = 4,
  cut = 12,
 &end
 &ewald
  eedmeth= 5
 &end
 
 minimisation dans le vide avec Newton-Raphson
 &data
  ntrun = 1,
  drms = 0.0001,
  nvect = 2322,
  maxcyc = 1,
  scee = 1.2,
  dielc = 4,
  cut = 12
 &end
 &ewald
  eedmeth= 5
 &end
 
 Please help me !
 
 Thank you,
 
 Marie Brut
 LAAS-CNRS
 Toulouse, France

             
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