Hello All
I am doing MD simulation of protein-DNA complex but at the beginning of
production run there is high fluctuation of terminal end residue as a
result it is making unusual non covalent bond with another residue (not
observed in crystal structure) also affecting other non covalent bonds.
To resolve it I want to use NMR restraint so that it will show little
fluctuation.
I amber tutorial there is a tutorial for NMR restraint, generation of
distance & torsion angle restraint is already defined here.
Distance_restraint:-
1
st
_res# 1
st
_res_name 1
st
_atom_name 2
nd
_res# 2
nd
_res_name 2
nd
_atom_name upper_bound
Torsion angle restraint:-
res# res_name torsion_name lower_bound upper_bound
But here I am not getting how to define upper_bond in "Distance
restraint" and lower_bond and upper_bond in "Torsion angle restraint"
Can anyone please help me to get it.
With regards
Sangita Kachhap
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Received on Tue Aug 20 2013 - 22:30:03 PDT
