MD,discover,H-bond,help
Dear Netters,
Could you please try to help a friend of mine with the following:
I am trying to run Discover with Amber force field.
It seems that the minimization makes my initial B_DNA_Duplex
structure (7 nucleotide-pairs) fall apart. What should
I do to avoid that? Is there a way to avoid the hydrogen bonds
get apart?
Here is the input file. I can send you the .car
and the .mdf files if you wish to take a look
-----------------------------Input file-----------------------
overlap = 0.01
cutoff = 12.000000
cutdis = 11.000000
swtdis = 1.5
begin simulation
* add-automatic bond torsion valence out-of-plane
reduce
scale 1-4 parameters by 0.500000
set dielectric = 4.000000*r
Minimize
* no cross terms
* no morse
* for 10000 iterations
* using conjugate gradient
* until the maximum derivative is less than 0.001000000 kcal/A
end
------------------------------------------------end of input file
Any help is highly appreciatted.
Thanks,
Monica