Re: AMBER: NMR refinement

From: Wenyong Tong <wenyong_tong.yahoo.com>
Date: Fri, 28 Sep 2007 12:29:30 -0700 (PDT)

Hello, David

Thank you for suggestions.

(1) I only input part of distance restrains because MD
just stopped if given all of restrains. I guessed some
of assignments were not right.
(2) It seems that the format of my “anneal.in” file
had some problems.
(3) I run a short time annealing with new .in files.
Result seems ok. Any suggestions for this?
===============================================================================

   KE Trans = 0.0000 KE Rot = 0.0000
C.O.M. Vel = 0.000000

   Translational and rotational motion removed

   KE Trans = 0.0000 KE Rot = 0.0000
C.O.M. Vel = 0.000000

 NSTEP = 550000 TIME(PS) = 1100.000 TEMP(K) =
  24.27 PRESS = 0.0
 Etot = -114.4606 EKtot = 10.6366
EPtot = -125.0971
 BOND = 15.5273 ANGLE = 34.3019
DIHED = -35.8702
 1-4 NB = 32.3989 1-4 EEL = 1137.2888
VDWAALS = -48.6193
 EELEC = -760.3267 EGB = -499.8236
RESTRAINT = 0.0258
 EAMBER (non-restraint) = -125.1229

------------------------------------------------------------------------------

 NMR restraints: Bond = 0.026 Angle = 0.000
Torsion = 0.000
===============================================================================

      A V E R A G E S O V E R 550000 S T E P S


 NSTEP = 550000 TIME(PS) = 1100.000 TEMP(K) =
 909.62 PRESS = 0.0
 Etot = 458.2530 EKtot = 398.5732
EPtot = 59.6798
 BOND = 59.2379 ANGLE = 133.2183
DIHED = -15.3631
 1-4 NB = 38.7507 1-4 EEL = 1129.0126
VDWAALS = -40.8537
 EELEC = -732.1089 EGB = -512.7310
RESTRAINT = 0.5171
 EAMBER (non-restraint) = 59.1627

------------------------------------------------------------------------------

 NMR restraints: Bond = 0.026 Angle = 0.000
Torsion = 0.000
===============================================================================

      R M S F L U C T U A T I O N S


 NSTEP = 550000 TIME(PS) = 1100.000 TEMP(K) =
 228.70 PRESS = 0.0
 Etot = 139.8929 EKtot = 100.2091
EPtot = 43.2414
 BOND = 12.9421 ANGLE = 24.8968
DIHED = 5.8055
 1-4 NB = 3.7961 1-4 EEL = 16.8955
VDWAALS = 3.8772
 EELEC = 23.5680 EGB = 16.1573
RESTRAINT = 0.7451
 EAMBER (non-restraint) = 42.4962

------------------------------------------------------------------------------





--- "David A. Case" <case.scripps.edu> wrote:

> On Wed, Sep 26, 2007, Wenyong Tong wrote:
> >
> > Could you please give some suggestions about the
> > following results from NMR refinement? Please note
> > that the final temperature did not get down.
>
> You should examine the beginning of the input file,
> where the program prints
> out the weight change information: be sure it seems
> to do what you want.
>
> I don't see anything obviously wrong with the input,
> but I'm probably missing
> something. But try some short(!) test cases to make
> sure annealing is doing
> what you want -- something like 1,000 to 10,000
> times shorter than what you
> showed here.
>
> >
> > NMR restraints: Bond = 0.045 Angle =
> 0.000
> > Torsion = 0.000
>
> Note that even without cooling, you have essentially
> zero restraint
> violations. I have no idea whether this means that
> your structures are really
> good, or that your restraints are too weak, but it
> is something to look into.
>
> ...dac
>
>
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Wenyong




       
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