Dear amber users,
I am trying to calculate the RDF and Coordination Number of an
electronegative atom, N7 of the DNA with respect to the Mg2+ ions present
in the system.
These are the following commands :
>parm dna-mg.prmtop
>trajin prod100ns.nc
>radial out rdf-4n7-maj.txt :4.N7 :MG 0.1 40 volume intrdf
intrdf-4n7-maj.txt
>go
>quit
and the output which i got, here are the some initial outcomes after 2
angstrom for both the cases , *first and third column are the distances and
second and fourth column are rdf and CN respectively . Here (rdf is
correct) CN is incorrect* and I don't know why it is like this .
#Distance_(Ang) :4.N7_=>_:MG #Distance_(Ang) Int[:MG]
2.050000 0.000000 2.050000 0.000000
2.150000 0.000000 2.150000 0.000000
2.250000 0.000000 2.250000 0.000000
2.350000 0.000000 2.350000 0.000000
2.450000 0.000000 2.450000 0.000000
2.550000 0.000000 2.550000 0.000000
2.650000 0.000000 2.650000 0.000000
2.750000 0.000000 2.750000 0.000000
2.850000 0.000000 2.850000 0.000000
2.950000 0.000000 2.950000 0.000000
3.050000 0.000000 3.050000 0.000000
3.150000 0.000000 3.150000 0.000000
3.250000 0.000000 3.250000 0.000000
3.350000 0.000000 3.350000 0.000000
3.450000 0.000000 3.450000 0.000000
3.550000 0.000000 3.550000 0.000000
3.650000 0.223464 3.650000 0.000005
3.750000 0.846824 3.750000 0.000024
3.850000 2.209368 3.850000 0.000078
3.950000 5.151902 3.950000 0.000210
4.050000 9.619777 4.050000 0.000468
4.150000 16.162764 4.150000 0.000924
4.250000 20.520724 4.250000 0.001532
4.350000 25.094831 4.350000 0.002310
4.450000 21.273521 4.450000 0.003000
4.550000 17.400684 4.550000 0.003590
4.650000 10.670881 4.650000 0.003968
4.750000 6.795559 4.750000 0.004220
4.850000 3.733743 4.850000 0.004363
*-------------------------------------------------*
*With Regards*
*Angad Sharma*
*Research Scholar*
*School of Computational & Integrative Sciences*
*Jawaharlal Nehru University*
*New Delhi 110067, (INDIA)*
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Sun Apr 09 2023 - 15:30:02 PDT
