Hi
many thanks indeed.
I have a silly question, I can see in page 254 of amber9 manual the command:
radial root-filename spacing maximum solvent-mask [solute-mask] [closest]
[density value] [noimage]
Later in that paragraph it says:
"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."
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 122-5073)
i guess it is 122-5073!
so this ptraj command will give me: interation of 122-5073 with every 122-5073?
probably solute-mask should be replaced by solvent-mask in
"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."
??
"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
________________________________
From: Thomas Cheatham III <tec3.utah.edu>
To: AMBER Mailing List <amber.ambermd.org>
Sent: Tue, July 27, 2010 4:39:29 PM
Subject: Re: [AMBER] RDF 3 files and 3 columns
> my molecule ha 121 residues the rest is water which makes the whole system 5073
>
> residues, i.e 17100 atoms.
> My solvent mask should be 14756 atoms (water), but below ptraj says: "
>Solvent
>
> atom selection is :1.N76,:122-5073" because solvent is just 122-5073!
As mentioned, you need to read up on the syntax of atom selection; solvent
should be 14856 atoms... You have selected that and also :1.N76
> my other question, you mentioned in your email "distance RDF-value integral"
> what is this please?
> ________________
> trajin pdb_bond_wat_md1_exp.mdcrd
> trajin pdb_bond_wat_md2_exp.mdcrd
> center :1-5073 origin mass
> image origin center familiar
> radial pdb_bond_wat_rad_dens.rdf 0.5 10.0 :WAT:1.N76 density 0.033456
You likely just want to center the solute, :1-121, not the entire box,
prior to imaging.
center :1-121 mass origin
> PTRAJ: radial pdb_bond_wat_rad_dens.rdf 0.5 10.0 :WAT:1.N76 density 0.033456
> Mask [:WAT:1.N76] represents 14857 atoms
> [No output trajectory specified (trajout)]
Yep, (5073 - 121)*3 + 1 extra atom selected... It is so slow since it is
doing the PMF of every atom to every atom (in your selection).
Add a space between selections; also you likely do not want the RDF to
water but separate RDF's of water oxygen's or hydrogens...
radial out 0.5 10.0 :WAT.O :1.N76
--tec3
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Received on Tue Jul 27 2010 - 10:00:03 PDT
