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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Received on Sun Jun 17 2007 - 06:07:07 PDT
