sir,
is the command below ok for dna in explicit water?
center :1-20 mass origin
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
On Sat, Sep 7, 2013 at 9:46 PM, Daniel Roe <daniel.r.roe.gmail.com> wrote:
> Hi,
>
> On Sat, Sep 7, 2013 at 1:19 AM, Mary Varughese <maryvj1985.gmail.com>
> wrote:
> > sir,
> > On doing hbond analysis (including solvent effect), should i image
> center
> > familiar solvent residues also? (simulation is done with iwrap=1). would
> it
> > affect my analysis.
>
> If you are looking for solvent-solute hydrogen bonds you should
> definitely reimage prior to 'hbond' since neither ptraj nor cpptraj
> use imaged distances in the 'hbond' command; in cpptraj I recommend
> using 'autoimage' for this purpose.
>
> -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 Sun Sep 08 2013 - 19:30:02 PDT
