You never defined an equilibrium distance or force constant for your
restraint, all of which default to 0, I think. Therefore, you will get no
restraint energy, and an absolutely flat potential everywhere (as though you
added no restraints at all).
Good luck!
Jason
On Fri, Sep 17, 2010 at 2:32 AM, tong Zhu <z5476t4508.gmail.com> wrote:
> Hello everyone!
>
> I am using AMBER11 and trying to restraint the distance of the Mg2+ (in the
> residue 361) and the N1 atom (in the residue 362) during the minimization.
> the input file is:
>
> initial minimisation
> &cntrl
> imin = 1,
> maxcyc = 80000,
> ncyc = 40000,
> ntb = 1,
> ntr = 0,
> cut = 10.0,
> nmropt = 1,
> /
> &wt type='END' /
> LISTOUT=POUT
> DISANG=RST
>
> and the RST file is:
>
> &rst
> restraint = "distance( :361.MG :362.N1)"
> &end
>
>
> But when I check the output structure, the distance which is supposed to be
> fixed, actually changed. Did I do something wrong or not successfully
> define
> the restraint?
>
> the part of the output file is:
>
>
> FINAL RESULTS
>
>
>
> NSTEP ENERGY RMS GMAX NAME NUMBER
> 50573 -1.7210E+05 6.6024E-03 3.6550E-01 O 10450
>
> BOND = 12476.7063 ANGLE = 1252.4266 DIHED =
> 3454.6525
> VDWAALS = 28824.6341 EEL = -226238.3125 HBOND =
> 0.0000
> 1-4 VDW = 1240.0958 1-4 EEL = 6892.2751 RESTRAINT =
> 0.0000
> NMR restraints: Bond = 0.000 Angle = 0.000 Torsion = 0.000
>
> ===============================================================================
>
> ------------------------------------------------------------------------------
>
>
> Final Restraint Analysis for coords: min2.rst
>
>
> Restraints, deviations, and energy contributions: pencut = 0.10
>
>
> ------------------------------------------------------------------------------
> First atom Last atom curr. value target deviation penalty
>
> ------------------------------------------------------------------------------
>
> ------------------------------------------------------------------------------
>
>
> Could anybody give me some suggestions? Many thanks!
> ******
> **
> *
> *
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>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-4032
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Received on Fri Sep 17 2010 - 04:30:04 PDT
