On Mon, 2014-04-14 at 09:51 +0200, Urszula Uciechowska wrote:
> 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.
The center of your umbrella potential is at 13.8 Angstroms. Was this
intentional?
If atoms 3457 and 4153 are NOT the H-bonding pair of atoms, then you'll
have to rationalize why the hydrogen bond is broken based on insight you
can gain by analyzing the trajectory and force field. If atoms 3457 and
4153 ARE the H-bonding pair of atoms, then your restraints are forcing
them apart.
HTH,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Mon Apr 14 2014 - 05:30:02 PDT
