Dear Amber Users,
I'm using "radial" function with both ptraj and cpptraj (AT-13 with
all latest bugfixes to date) to estimate the number of water molecules
(:WAT) around a residue of my protein (:92).
After loading 10 frames from my simulation I used the following commands:
with PTRAJ
> image
> radial pt_2 0.2 15.0 :WAT :92 noimage
> radial pt_1 0.1 15.0 :WAT :92 noimage
with CPPTRAJ
> radial cppt_02.out 0.2 15.0 :WAT :92 intrdf cppt_02.out
> radial cppt_01.out 0.1 15.0 :WAT :92 intrdf cppt_01.out
>From the mailing list I understood that the last column in ptraj
output represents the integral (or effectively the occupancy as a
function of distance or loosely how many waters in a shell of a given
radius), and also with the "intrdf" option I expect cpptraj to print
the same information in the output file.
Comparing the outputs from ptraj (standard normalization) and cpptraj
I saw that the RDF values are in agreement with each other, as
expected, but that the integral values are very different.
Also, doubling the bin spacing leads to a doubling of the integral
values in cpptraj output, while integral values from ptraj are almost
unchanged.
I also approximated by hand the integral with the trapezoid rule (from
the RDF values), and I obtained a reasonable result with both 0.1 and
0.2 bin spacing.
So, in conclusion, I'm asking if someone in the list can clarify to me
why the integral values are so different from ptraj and cpptraj, and
on which value I have to rely to have an approximation of the number
of water molecules around my residue.
Thank you in advance for any help,
Domenico
--
Domenico Marson
Ph.D. student
Molecular Simulation Engineering (MOSE) Laboratory
Department of Engineering and Architecture - DEA
University of Trieste
Via Valerio, 10
34127 - Trieste (Italy)
Phone: +39 040 5583757
Skype: domenicomars
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Received on Tue Jun 18 2013 - 10:00:02 PDT
