thank you very much
On Mon, Sep 9, 2013 at 10:24 PM, Daniel Roe <daniel.r.roe.gmail.com> wrote:
> Hi,
>
> On Mon, Sep 9, 2013 at 3:20 AM, Mary Varughese <maryvj1985.gmail.com>
> wrote:
> > Is there any need to do a "mass weighted backbone RMS fit of every frame
> to
> > the first frame in the trajectory" before performing hbond analysis(by
>
> No.
>
> > ptraj). Also on analysing solvent interaction with the system ( dsDNA).
> is
> > it sufficient to reimage like (used iwrap=1)
> >
> > center :1-20 mass origin// dna
> > image origin center familiar
> > center :1-38 mass origin //Na ions
> > image origin center familiar
> > center :1-5529 mass origin// water residue
> > image origin center familiar
>
> This is incorrect, particularly the last 4 commands. First, I *highly*
> recommend you use the 'autoimage' command in cpptraj for this; it was
> specifically designed to take all of the guesswork out of re-imaging a
> trajectory. However, if you're dead-set on doing it yourself, this has
> worked for me in the past:
>
> center :L-M origin mass
> image center origin
> center :L-N origin mass
> image center origin
>
> This assumes you have double-stranded DNA from residues L to N where L
> is the first residue of your first DNA strand, M is the last residue
> of the first strand, and N is the last residue of the second strand.
>
> > Also if i have to strip water residues at a distance greater than 3.6
> > angstrom;
> >
> > would it be ok to have all these in a single script.
>
> It is if you do the stripping of the solvent last. Without knowing why
> you want to strip the water though it's tough to make an exact
> recommendation. See the 'mask' command in cpptraj for writing out
> structures with distance-based masks. Also of interest may be the
> 'closest' command, which will keep a certain # of waters close to a
> specified mask.
>
> > I dont want to create another prmtop.
>
> Unless you use the closest command or you are very lucky, if you strip
> just based on distance there is no guarantee the resulting systems
> will have the same # of atoms, so you will probably have to make
> another topology to process these structures. The 'mask' command will
> output PDB files which are essentially their own topology, so you may
> have luck using that command.
>
> Hope this helps,
>
> -Dan
>
> --
> -------------------------
> Daniel R. Roe, PhD
> Department of Medicinal Chemistry
> University of Utah
> 30 South 2000 East, Room 201
> Salt Lake City, UT 84112-5820
> http://home.chpc.utah.edu/~cheatham/
> (801) 587-9652
> (801) 585-9119 (Fax)
>
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Received on Mon Sep 09 2013 - 18:00:02 PDT
