Daniel
Thanks...worked just fine:)
On Mon, Sep 1, 2014 at 8:41 PM, Daniel Roe <daniel.r.roe.gmail.com> wrote:
> Hi,
>
> On Mon, Sep 1, 2014 at 4:36 AM, DEBOSTUTI GHOSHDASTIDAR
> <debostutighosh.gmail.com> wrote:
> > hbond out test1.dat solventdonor :Na+ solventacceptor :1-24.O1P,O2P
> > nointramol solvout test.dat (where 1-24 are the residue numbers of the
> DNA
> > dodecamer)
>
> This isn't the correct way to use Hbond to track ions. You want both
> solvent masks set to ions, then provide another mask (or use the
> donormask/acceptormask keywords) for the solute, e.g.
>
> hbond out test1.dat solventdonor :Na+ solventacceptor :Na+ \
> :1-24.O1P,O2P nointramol solvout test.dat
>
> Also, be careful that you are using the correct atom names. The
> phosphate oxygens may be named OP1/OP2. You can check this easily by
> running cpptraj with the '--mask' command-line flag, e.g.:
>
> cpptraj <topology file> --mask '.O1P'
>
> Hope this helps,
>
> -Dan
>
> >
> > In the output, however, I see that test.dat contains not only hbond
> > information between the O1P/O2P with Na+, but also those formed between
> > other atoms of the DNA and Na+.
> >
> > Hence, I assume that the information on solvent bridges given in the
> > test1.dat file include Na+ ions that bridge any two atoms of the DNA and
> > not just the phosphates.
> >
> > Any suggestions on how I can get the required information, i.e, only Na+
> > ions that bridge the phosphates?
> >
> > Thanks
> > --
> > Debostuti Ghosh Dastidar
> > Department of Biotechnology
> > Indian Institute of Technology Madras
> > _______________________________________________
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>
>
>
> --
> -------------------------
> Daniel R. Roe, PhD
> Department of Medicinal Chemistry
> University of Utah
> 30 South 2000 East, Room 307
> Salt Lake City, UT 84112-5820
> http://home.chpc.utah.edu/~cheatham/
> (801) 587-9652
> (801) 585-6208 (Fax)
>
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>
--
Debostuti Ghosh Dastidar
Department of Biotechnology
Indian Institute of Technology Madras
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Received on Tue Sep 02 2014 - 09:30:02 PDT
