Re: MM-PGBSA Question!!

From: Lepsa <>
Date: Sat 22 Dec 2001 15:46:53 +0100

Hello Bernd,
I can try to answer only your first question:

The large fluctuations of energies among snapshots are the reality, I rather
wonder how the energies (e.g. interaction
energies differing by a couple of kcal/mol) can come out with qualitative
precision. The small deviations you can
sometimes see in the literature are "block" deviations, i.e. average of the
values of the 1st and 2nd half of production run.

Hope this helps,

  Martin Lepsik

> 1.)We performed several mm-pbsa calculations of DNA and
> although two simulations starting from different
> conformations exhibit a similar mean value (+- 1kcal/mol)
> of the free energy
> the standard deviations are extremly large (about 20 kcal/mol).
> The standard deviations of similar calculations (Srinivasan et al. 1998 )
> is much smaller while Wu et al. 2002 had comparable standard
> deviations. Does anyone have an idea why this happens, and is the
> calculation of small (about 10 kcal/mol) delta G still allowed.
> 2.) Wang et al. (2001) performed a normal mode analysis of a large
> protein and due to the size only the residues within 12 A of interest
> were used for the normal mode calculation. Does anyone know how they
> did this. Did they use ibelly for the other residues or did they cut out
> the part
> of interest.
> Thanks in advance Bernd Wellenzohn

From 26 Dec 2001 15:56:17 -0000
Message-id: <>
Date: 26 Dec 2001 15:56:17 -0000
From: Raja Swaminathan <>
To: AMBER list <>
Subject: ion analysis
In-Reply-to: <>

Dear ambers

I have done 2 ns MD on a 14 mer DNA duplex. I want to analyse the ions.

I have used the distance option in ptraj.
(i.e)I want to calculate the distance between a particular base atom for ex N6 and Na+ over the entire simulation for all the residues.

The input what i have given looks like this

distance name .Na+ 1_at_N6 noimage
distance name .Na+ 2_at_N6 noimage
distance name .Na+ 3_at_N6 noimage
distance name .Na+ 4_at_N6 noimage

But the output shows the nan error at some of the places and some values for some. I don't know how where i went wrong. Please give some suggestions regarding this.

Thanking you in advance

Raja Swaminathan

Received on Sat Dec 22 2001 - 06:46:53 PST
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