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.scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu
Received on Sun Jun 17 2007 - 06:07:08 PDT
