Hello Dr. Case,
Was this recommended to you for sugars or something?
No.
Today, I run an annealing as you suggested.
NSTEP = 100000 TIME(PS) = 400.000 TEMP(K) = 5.85 PRESS = 0.0
Etot = 152.2650 EKtot = 2.5613 EPtot = 149.7037
BOND = 17.4697 ANGLE = 66.4454 DIHED = -12.7984
1-4 NB = 49.4192 1-4 EEL = 1105.4033 VDWAALS = -27.3679
EELEC = -715.6464 EGB = -505.0644 RESTRAINT = 171.8433
EAMBER (non-restraint) = -22.1395
H4 4GB 2 -- H2 4GB 2: 3.751 2.070 1.681 18.038 d 0: 0
Total distance penalty: 171.411
| RMS deviation from ideal bonds : 0.0216
| RMS deviation from ideal angles : 3.569
There are some distances with high penalty. I deleted about 10 violations. I got the following results. I wonder whether it is appropriate to delete them. I know two NOE assignments are ambiguous, but how about others? Should the final Eptot be minus?
NSTEP = 100000 TIME(PS) = 400.000 TEMP(K) = 5.77 PRESS = 0.0
Etot = -15.6114 EKtot = 2.5271 EPtot = -18.1386
BOND = 16.1804 ANGLE = 54.6413 DIHED = -14.7677
1-4 NB = 45.3959 1-4 EEL = 1126.9869 VDWAALS = -35.7446
EELEC = -752.6347 EGB = -493.8424 RESTRAINT = 35.6463
EAMBER (non-restraint) = -53.7849
------------------------------------------------------------------------------
NMR restraints: Bond = 35.646 Angle = 0.000 Torsion = 0.000
===============================================================================
Have a nice weekend.
Wenyong
----- Original Message ----
From: David A. Case <case.scripps.edu>
To: amber.scripps.edu
Sent: Friday, January 18, 2008 12:35:37 PM
Subject: Re: AMBER: NMR refinement
On Fri, Jan 18, 2008, David A. Case wrote:
I missed one other thing:
> On Thu, Jan 17, 2008, Wenyong Tong wrote:
> >
> > igb=1, saltcon=0.05, offset=0.13,
^^^^^^^^^^^
Why are you setting your own offset??? I would guess that this would
mess
up the GB energetics of your system quite a bit. Changing this from
the
default value is certainly a very advanced step -- was this recommended
to you
for sugars or something?
...dac
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Received on Sun Jan 20 2008 - 06:07:30 PST
