Respected Sir,
I have carried out a 2ns MD simulation on a 14mer DNA duplex.I would like to
analyse the ion and water distribution around the DNA.
I see from one of the papers ( JACS, (1997) 119, 4805- )that they have done
that by binning atom positon from RMS coord's fit frames at
1ps interval into 0.5A^3 grids for a 1ns run. Then they have calculated
the number of times any coord' of the centre of a water oxygen of interest
were within the 0.5A^3 respresented by a particular grid element.Then
contouring has been done using MidasPlus.
Is there any particular program provided along with AMBER 6.0 that does
this.Please give me some suggestion in this regards.
Thanking you
Prem Raj
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Received on Thu Dec 21 2000 - 08:12:53 PST
