On Mon, Apr 14, 2014, Urszula Uciechowska wrote:
>
> I tried to keep a h-bond between two atoms (DNA and protein) during my MD.
> In order to do this I introduce nmropt restraints. However after heating I
> do not see the H-bbond any more.
>
>
> &rst iat=3457,4153
> r1=0,r2=13.8,r3=13.8,r4=100.0,rk2=10.0,rk3=10.0, /
> &end
This restraint should keep the distance between atoms 3457 and 4153 near
13.8 Ang. That doesn't sound anything like a hydrogen bond. See what
distance you actually get (e.g. by using the distance command in cpptraj).
Also, look at the output to see if the restraints were read correctly
(setting LISTIN=POUT can help). Make sure that you have a non-zero
RESTRAINT energy.
...dac
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Received on Mon Apr 14 2014 - 05:30:03 PDT
