AMBER Archive (2004)

Subject: Re: AMBER: H-bonded waters selection

From: pl (ladam_at_smbh.univ-paris13.fr)
Date: Fri Nov 05 2004 - 04:42:01 CST

Dera Thomas,
Thank you for this long and precise answer. Well I did not realize I
went into such a big process...
Basicaly, my thoughts where that I could use a file generated by the
'ptraj hbond' command to get a list of H-Bonded waters to dna PER FRAME
(which I did not manage to do yet).
Second, by some scripting in VMD I would (hopefully) display dna +
H-bonded waters from per frame the list above.
Is this 'per frame option' available with ptraj hbond ?

Bye and thanks again

Le jeudi 04 novembre 2004 à 22:05 -0700, Thomas E. Cheatham, III a
écrit :
> > I have a trajectory of solvated DNA and I want to analyse the hydration
> > of my DNA. For this I'd like to re-save this trajectory with the DNA
> > plus the water molecules that are H-bonded to it (that is get rid of
> > waters not H-bonded to DNA and visualize with VMD). I tried to play
> > around with ptraj and the trajout command but could not acheive that.
>
> There are two general ways to do this with ptraj.
>
> (1) closest
>
> You can save the closest "N" waters to the DNA; this will create a new
> trajectory of the DNA plus N waters. To view it with VMD, you would have
> to either create a prmtop with that many waters or a PDB with that many
> waters to load up prior to loading the trajectory. Note that water
> residue numbers are not retained, i.e. waters are ordered now 1->N rather
> than by their original numbers so it is not possible to "track" individual
> waters with the post-processed trajectory (i.e. use commands like
> diffusion).
>
> closest 100 :1-10
>
> will save the closest 100 waters around residues 1-10. Note that DNA
> normally has a minimal hydration of something like 20 waters per base
> pair (if I am remembering correctly).
>
> (2) grid
>
> It is possible to grid "atomic density" (used loosely here, realistically
> what is binned is a count of selected atoms per grid element) around the
> DNA and view this with chimera (available from the Computer Graphics Lab
> at UCSF loading up an Xplor density file). This a really nice way to see
> where tight waters, etc. are located.
>
> a. center/image the water around the area of interest
> b. rms fit to a common reference frame
> c. grid the water (or ion) density
>
> In a second run, do steps (a) and (b) and output a reference PDB (i.e. the
> first frame) which average structures can be fit to and therefore
> correspond to the grid.
>
> Here is a portion of a ptraj input file that I use to construct a grid
> around a portion of a double stranded DNA. My duplex has 22 base pairs.
>
> trajin traj.37.gz
> trajin traj.38.gz
> trajin traj.39.gz
> trajin traj.40.gz
>
> center :1-22 mass origin
> image origin center familiar
> center :1-44 mass origin
> image origin center familiar
> rms first mass out rms :1-44
> rms first mass out rms.middle :10-13,:32-35
> grid wat.grid 100 0.5 100 0.5 120 0.5 :WAT_at_O
> grid na.grid 100 0.5 100 0.5 120 0.5 @Na+
> grid cl.grid 100 0.5 100 0.5 120 0.5 @Cl-
>
> strip :45-99999
>
> average avg_0-5ns.pdb :1-44 pdb start 0 stop 5000
> average avg_5-10ns.pdb :1-44 pdb start 5000 stop 10000
> average avg_10-15ns.pdb :1-44 pdb start 10000 stop 15000
>
> Note that dynamics of the molecule will smooth the grid (i.e. lower the
> effective density). It takes a while to get a feeling for what the grid
> represents.
>
>
> I hope this helps.
>
> p.s. you can also look at radial distribution functions, the hbond
> routines to look at lifetimes of bound water, ...
>
>
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