AMBER Archive (2008)

Subject: Re: AMBER: NMR refinement

From: Wenyong Tong (wenyong_tong_at_yahoo.com)
Date: Fri Jan 18 2008 - 22:18:18 CST

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_at_scripps.edu>
To: amber_at_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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