Hi
I run RDF to see distribution of macromolecule (:1-121) wrt to center :1.H19.
And then to see distribution of water(:WAT.O) wrt to center :1.H19
trajin pdb_bond_wat_md1_exp.mdcrd
trajin pdb_bond_wat_md2_exp.mdcrd
trajin pdb_bond_wat_md3_exp.mdcrd
center :1-121 mass origin
image origin center familiar
radial pdb_bond_wat_rad_dens.rdf 0.5 40.0 :1.H19 :1-121 density 0.033456
trajin pdb_bond_wat_md1_exp.mdcrd
trajin pdb_bond_wat_md2_exp.mdcrd
trajin pdb_bond_wat_md3_exp.mdcrd
center :1-121 mass origin
image origin center familiar
radial pdb_bond_wat_rad_dens_wat.rdf 0.5 40.0 :WAT.O :1.H19 density 0.033456
all volume and standard files give me RDF=0, only carnal has got some non zero
values in both cases!
how do I get the density from carnal, what unit it is?
I really do not what carnal is, am using amber9.
Thanks for any help
________________________________
From: Thomas Cheatham III <tec3.utah.edu>
To: AMBER Mailing List <amber.ambermd.org>
Sent: Tue, July 27, 2010 6:11:15 PM
Subject: Re: [AMBER] RDF 3 files and 3 columns
> "If only a solvent-mask is listed (i.e. a list of atoms) then the RDF will be
> calculated for the interaction of every solute-mask atom with ALL the other
> solute mask
> atoms."
Think of a bulk solution of water. To calculate the radial
distribution function, you could look at the RDF of 1 water
with all the others; however, much better statistics will be obtained by
doing all waters to all waters. Try it out and see...
radial one-wat.rdf 0.5 40.0 :WAT.O :122.O
vs.
radial all-wat.rdf 0.5 40.0 :WAT.O
The latter will be smoother.
> Does this mean, if I specify: radial pdb_bond_wat_rad_dens.rdf 0.5 40.0
> :1-121 density 0.033456 Solvent mask is (:1-21) ? what would be the
> solute then? (my macromolecule is from residu 1-121, water from residu
I think confusion is definition of solvent and solute here which are
arbitrary. If you only specify one atom selection (or mask) you would
calculate the RDF of all the atoms in :1-121 with all of the other atoms
in :1-121 and likely would not be that meaningful...
If two masks are specified, the RDF is of the atoms in the first selection
around the atoms in the second selection.
> "If the optional solute-mask is specified, then the RDF will represent
> the interaction of each solute-mask atom with ALL of the solvent-mask
> atoms." This later paragraph if i quite understand means that when i
> specify radial pdb_bond_wat_rad_dens.rdf 0.5 40.0 :WAT.O :1-121 density
> 0.033456 will give me interaction of each :1-121 with all :WAT.O
Yes, however again you will find this is not so meaningful or easy to
interpret. Much easier to interpret is either the bulk solvent RDF, or
the RDF with respect to a particular atom. If I understand your case, you
wanted to see water "inside" the solute, therefore your atom of choice for
the RDF should be an atom closest to the center (or the code should be
changed to allow an RDF with respect to the origin). -tec3
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Received on Thu Jul 29 2010 - 13:00:04 PDT
