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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Received on Sun Sep 30 2007 - 06:07:43 PDT
