I think you need to add the weight in your input file, like the one below:
&wt type='REST', istep1=0,istep2=0,value1=1.0, value2=1.0, /
&wt type='END' /
Include also the following line right below DISAND:
LISTOUT=POUT
Also, is the atom numbers 1937 and 6833 the atoms you want restrain? The
distance criteria you have is pretty wide (from 1 to 5.30 Angstrom). Is
that what you want to do?
Best regards,
Ilyas Yildirim, Ph.D.
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On Thu, 18 Sep 2014, John Smith wrote:
> Hi AMBER users,
>
> I am trying to construct an adiabatic map for an enzyme ligand complex in
> which the ligand binds covalently to a residue in the protein. I am
> restraining a distance between a ligand atom and a protein atom over a
> range. My input file for minimization looks like this
>
> Initial minimisation
> &cntrl
> imin=1, maxcyc=2000, ncyc=1000,
> cut=12, ntb=1, igb=0, nmropt=1,
> &end
> &wt
> type='END',
> &end
> DISANG=RST-8.dist
>
> and the distance file is
>
> #
> # 123 CYM SG 432 UNK C38 1.0 5.3 &rst
> ixpk= 0, nxpk= 0, iat=1937,6833, r1= 0.50, r2= 1.00, r3= 5.30, r4= 5.80,
> rk2=20.0, rk3=20.0, ir6=1, ialtd=0,
> &end
>
> When I run the minimization I only get zero values for the restrain like
> this:
>
> NSTEP ENERGY RMS GMAX NAME NUMBER
> 1 -1.2114E+05 2.2113E+01 1.2152E+03 O 20311
>
> BOND = 1257.6726 ANGLE = 2422.4741 DIHED =
> 4450.7597
> VDWAALS = 13925.5850 EEL = -161068.9140 HBOND =
> 0.0000
> 1-4 VDW = 1614.9207 1-4 EEL = 16259.9956 RESTRAINT =
> 0.0000
> NMR restraints: Bond = 0.000 Angle = 0.000 Torsion = 0.000
>
> What could have gone wrong?
>
> Many thanks,
> Mahmood Jasim
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Received on Thu Sep 18 2014 - 05:00:10 PDT
