Hello and thanks a lot for all the information.
I run my following script: (it is still running actually)
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!
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
________________
And ptraj output is:
PTRAJ: Processing input from "STDIN" ...
PTRAJ: trajin pdb_bond_wat_md1_exp.mdcrd
PTRAJ: trajin pdb_bond_wat_md2_exp.mdcrd
PTRAJ: center :1-5073 origin mass
Mask [:1-5073] represents 17100 atoms
PTRAJ: image origin center familiar
Mask [*] represents 17100 atoms
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)]
PTRAJ: Successfully read the input file.
Coordinate processing will occur on 600 frames.
Summary of I/O and actions follows:
INPUT COORDINATE FILES
File (pdb_bond_wat_md1_exp.mdcrd) is an AMBER trajectory (with box info) with
100 sets
File (pdb_bond_wat_md2_exp.mdcrd) is an AMBER trajectory (with box info) with
500 sets
NO OUTPUT COORDINATE FILE WAS SPECIFIED
ACTIONS
1> CENTER to origin via center of mass, atom selection follows * (All atoms
are selected)
7> IMAGE familiar by molecule to origin using the center of mass, atom
selection * (All atoms are selected)
IMAGE familiar, center is at origin
7> RADIAL DISTRIBUTION FUNCTION: Output to pdb_bond_wat_rad_dens.rdf
spacing is 0.500
maximum is 10.000
[This implies 20 bins]
density is 0.033
RDF will represent all atoms in the solvent mask
Solvent atom selection is :1.N76,:122-5073
Processing AMBER trajectory file pdb_bond_wat_md1_exp.mdcrd
Set 1 .................................................
Set 50 ......................................
________________________________
From: Thomas Cheatham III <tec3.utah.edu>
To: AMBER Mailing List <amber.ambermd.org>
Sent: Mon, July 26, 2010 11:49:24 PM
Subject: Re: [AMBER] RDF 3 files and 3 columns
> I used ptraj for this. I have got 3 .xmgr files generated: volume, standard and
>
> carnal.
"carnal" is for backward compatibility. Volume uses the system volume to
normalize, whereas the "standard" uses the density to normalize.
Essentially, you want the RDF to go to unity (1.0) at longer distances (of
course this may not occur in small boxes since periodic imaging is not
currently performed).
> I looked up in the manual amber9, and in the mailing list but I cannot find the
>
> meaning of the 3 columns in each file. I am interested in plotting the radial
distance RDF-value integral
> density distribution of water HOH inside my macromolecule versus R.
> I want to use the center of mass of the macromolecule as the reference. I
> performed explicit solvent MD.
There is not code implemented to do this at present; it would not be so
difficult to modify the code to allow calculation of the RDF relative to
the origin (where the molecule could be centered).
I had not thought of tracking water inside a molecule, however I actually
have a need to do this in some older work.
As written the code will only do the RDF to a specific atom, to all the
atoms at once, or to only the atom in a mask that is closest to the water.
If you do not want to edit the code, an approximate way to do this,
assuming the core is not particularly mobile:
(1) center the molecule to the origin
(2) create a pdb file
trajin pdb_bond_wat_md1_exp.mdcrd 1 1 1
trajout vis.pdb pdb
center :1-121 mass origin
(3) add a dummy ATOM entry at the origin to the PDB
Add a line to the bottom of the PDB such as:
ATOM 0 X XXX 0 0.000 0.000 0.000
(4) visualize to find the atom that is closest to this dummy atom .X
let's assume it is :43.CA
(5) calculate the RDF around this atom.
trajin pdb_bond_wat_md1_exp.mdcrd
trajin pdb_bond_wat_md2_exp.mdcrd
center :1-121 mass origin
image origin center familiar
radial pdb_bond_wat_rad_dens.rdf 0.5 40.0 :WAT :43.CA
I'll think about adding the options for "origin" (since when combined with
the center command does the COM implicitly).
--tec3
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Received on Tue Jul 27 2010 - 07:00:04 PDT
