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From: cgji <cgji.itcc.nju.edu.cn>

Date: Mon, 24 Sep 2007 21:13:36 +0800

Dear Amber users,

Recently I tried to use molecular dynamics free energy simulations (MDFE) to compute proton pka

shifts as described in amber tutorial (http://amber.scripps.edu/tutorials/advanced/tutorial6/index.htm).

This tutorial reproduces the calculation of the pKa value of the ASP residue in the protein thioredoxin as described in the following paper:

Simonson, T., Carlsson, J., Case, D.A., "Proton Binding to Proteins: pKa Calculations with Explicit and Implicit Solvent Models", JACS 2004, 126, pp4167-4180.

In table 1 of the article ,they showed us expilicit solvent MDFE results for Thioredoxin ASP26 .

Part of this table was listed bellow ,

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

AMBER

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

ASP26

lamba=0.11270 -3.1(12.0)

lamba=0.50000 -64.5(4.6)

lamba=0.88279 -131.4(7.8)

Delta G -66.0(3.9)

Delta,Delta G 9.1 (4.1)

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

12.0 ,4.6 and 7.8 in parentheses was statistical uncertainty for the three

seperated trajectory .

My question is :

1.how can I estimate statistical uncertainty from each seperated trajectory ?

in their article , they said "for the derivatives , it is estimated as twice the standard derivation of block averages ,each trajectory being divided into four blocks." , however , i can't understand it clearly .

2. How can I use these data from seperated trajectory to construct statistical uncertainty (3.9) for

Delta G ?

I tried to calculate it as follows

sqrt ( (12.0*0.27777)**2+(4.6*0.44444)**2+(7.8*0.27777) **2)

but I can't get 3.9 .

I appreciate it very much for your help......

Yours sincerely,

Changge Ji

2007-09-24

cgji

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Received on Mon Sep 24 2007 - 17:45:26 PDT

Date: Mon, 24 Sep 2007 21:13:36 +0800

Dear Amber users,

Recently I tried to use molecular dynamics free energy simulations (MDFE) to compute proton pka

shifts as described in amber tutorial (http://amber.scripps.edu/tutorials/advanced/tutorial6/index.htm).

This tutorial reproduces the calculation of the pKa value of the ASP residue in the protein thioredoxin as described in the following paper:

Simonson, T., Carlsson, J., Case, D.A., "Proton Binding to Proteins: pKa Calculations with Explicit and Implicit Solvent Models", JACS 2004, 126, pp4167-4180.

In table 1 of the article ,they showed us expilicit solvent MDFE results for Thioredoxin ASP26 .

Part of this table was listed bellow ,

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

AMBER

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

ASP26

lamba=0.11270 -3.1(12.0)

lamba=0.50000 -64.5(4.6)

lamba=0.88279 -131.4(7.8)

Delta G -66.0(3.9)

Delta,Delta G 9.1 (4.1)

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

12.0 ,4.6 and 7.8 in parentheses was statistical uncertainty for the three

seperated trajectory .

My question is :

1.how can I estimate statistical uncertainty from each seperated trajectory ?

in their article , they said "for the derivatives , it is estimated as twice the standard derivation of block averages ,each trajectory being divided into four blocks." , however , i can't understand it clearly .

2. How can I use these data from seperated trajectory to construct statistical uncertainty (3.9) for

Delta G ?

I tried to calculate it as follows

sqrt ( (12.0*0.27777)**2+(4.6*0.44444)**2+(7.8*0.27777) **2)

but I can't get 3.9 .

I appreciate it very much for your help......

Yours sincerely,

Changge Ji

2007-09-24

cgji

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

The AMBER Mail Reflector

To post, send mail to amber.scripps.edu

To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu

Received on Mon Sep 24 2007 - 17:45:26 PDT

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