Dear Amber users,
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.
My input file:
Heating
&cntrl
imin = 0,
irest = 0,
ntx = 1,
cut = 9,
ntb = 1,
iwrap = 1,
nmropt = 1,
ntc = 2,
ntf = 2,
tempi = 0.0,
temp0 = 300.0,
ntt = 3,
gamma_ln = 1.0,
nstlim = 125000, dt = 0.002,
ntpr = 100, ntwx = 500, ntwr = 100,
/
&wt TYPE='DUMPFREQ', istep1=50,
/
&wt TYPE='END'
/
DISANG=dist.RST
LISTOUT=POUT
DUMPAVE=DISTout.RST.4
/
&end
The dist.RST file:
&rst iat=3457,4153
r1=0,r2=13.8,r3=13.8,r4=100.0,rk2=10.0,rk3=10.0, /
&end
Please guide me.
Thanks
Urszula Uciechowska
-----------------------------------------
Ta wiadomość została wysłana z serwera Uniwersytetu Gdańskiego
http://www.ug.edu.pl/
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Received on Mon Apr 14 2014 - 01:00:02 PDT
