Hi Daniel,
Thank you very much for explaining. Now it is clear to me.
Best,
indrajit
--------------------------------------------------------------------------------------------------------------
*Indrajit Deb*
alternate emails: indrajitdeb81.gmail.com, idbmbg_s.caluniv.ac.in
*Present Position*
International Centre for Genetic Engineering and Biotechnology (ICGEB,
Italy) SMART Fellow,
Department of Structural Chemistry and Biology of Nucleic Acids,
Institute of Bioorganic Chemistry (IBCh),
Polish Academy of Sciences (PAS).
European Center for Bioinformatics and Genomics (ECBiG) Campus (
R
oom: 2.6.28
).
Z. Noskowskiego Str. 12/14.
Poznan 61-704, Poland.
Phone: +48616653042, Personal Mobile: +48662513522
*Previous Position*
Ph.D Student,
Department of Biophysics, Molecular Biology and Bioinformatics, University
of Calcutta (CU), 92 APC Road, Kolkata - 700009, India. Phone:
+913323508386 (extn. 329, 321), Fax: +913323519755. Personal Mobile:
+919239202278
On Wed, May 11, 2016 at 6:49 PM, Daniel Roe <daniel.r.roe.gmail.com> wrote:
> Hi,
>
> On Wed, May 11, 2016 at 9:38 AM, Indrajit Deb <biky2004indra.gmail.com>
> wrote:
> > May be I misunderstood the meaning of the key 'first|oxygen'. I thought
> > that one can use either the key 'first' or 'oxygen'. If 'first' is used
> the
> > hydrogen or oxygen which is nearest will be considered, but if 'oxygen'
> is
> > used only the nearest oxygen atom will be considered.
>
> >From the Amber manual:
>
> [first | oxygen] Calculate distances between all atoms in <mask> and
> the first atom
> of solvent only (recommended for standard water models as it will increase
> speed of calculation).
>
> The 'oxygen' keyword is just an alias to 'first', and is kept for
> historical reasons (it has been this way since ptraj).
>
> Hope this clears things up,
>
> -Dan
>
> >
> > From your answer it seems that 'closest' command works according to atom
> > numbering where oxygen comes first.
> >
> > Please let me know If I again misunderstood.
> >
> > Best,
> > indrajit
> >
> >
> >
> >
> --------------------------------------------------------------------------------------------------------------
> > *Indrajit Deb*
> > alternate emails: indrajitdeb81.gmail.com, idbmbg_s.caluniv.ac.in
> > *Present Position*
> > International Centre for Genetic Engineering and Biotechnology (ICGEB,
> > Italy) SMART Fellow,
> > Department of Structural Chemistry and Biology of Nucleic Acids,
> > Institute of Bioorganic Chemistry (IBCh),
> > Polish Academy of Sciences (PAS).
> > European Center for Bioinformatics and Genomics (ECBiG) Campus (
> > R
> > oom: 2.6.28
> > ).
> > Z. Noskowskiego Str. 12/14.
> > Poznan 61-704, Poland.
> > Phone: +48616653042, Personal Mobile: +48662513522
> >
> > *Previous Position*
> > Ph.D Student,
> > Department of Biophysics, Molecular Biology and Bioinformatics,
> University
> > of Calcutta (CU), 92 APC Road, Kolkata - 700009, India. Phone:
> > +913323508386 (extn. 329, 321), Fax: +913323519755. Personal Mobile:
> > +919239202278
> >
> > On Wed, May 11, 2016 at 5:03 PM, Daniel Roe <daniel.r.roe.gmail.com>
> wrote:
> >
> >> On Wed, May 11, 2016 at 8:16 AM, Indrajit Deb <biky2004indra.gmail.com>
> >> wrote:
> >> > The following cpptraj output is showing that it considering the
> geometric
> >> > center between the selected atoms in the mask, but I want to consider
> the
> >> > oxygen atom of the water molecule to calculate the distance from the
> >> > geometric center. For that, I used the 'oxygen' key. But the output
> >> showing
> >> > that only first atom of the solvent molecule was used for distance
> >> > calculation.
> >>
> >> The first atom in a water molecule for most explicit water models
> >> (TIPXP, SPC, etc) is the oxygen. You can verify this yourself via
> >> something like:
> >>
> >> cpptraj -p <topology> --mask ':WAT' | head
> >>
> >> So I think things are OK. Is your output trajectory not what you
> >> expected? Maybe I'm just not understanding your question. Let me know
> >> if this doesn't clear things up.
> >>
> >> -Dan
> >>
> >> >
> >> >
> >> > CLOSEST: Finding closest 1 solvent molecules to atoms in mask
> :5.HN1
> >> ,O2P
> >> > Geometric center of atoms in mask will be used.
> >> > Only first atom of solvent molecule used for distance calc.
> >> >
> >> >
> >> >
> >> > Please explain what wrong I am doing.
> >> >
> >> > Best,
> >> > indrajit
> >> >
> >> >
> >> >
> >> >
> >>
> --------------------------------------------------------------------------------------------------------------
> >> > *Indrajit Deb*
> >> > alternate emails: indrajitdeb81.gmail.com, idbmbg_s.caluniv.ac.in
> >> > *Present Position*
> >> > International Centre for Genetic Engineering and Biotechnology (ICGEB,
> >> > Italy) SMART Fellow,
> >> > Department of Structural Chemistry and Biology of Nucleic Acids,
> >> > Institute of Bioorganic Chemistry (IBCh),
> >> > Polish Academy of Sciences (PAS).
> >> > European Center for Bioinformatics and Genomics (ECBiG) Campus (
> >> > R
> >> > oom: 2.6.28
> >> > ).
> >> > Z. Noskowskiego Str. 12/14.
> >> > Poznan 61-704, Poland.
> >> > Phone: +48616653042, Personal Mobile: +48662513522
> >> >
> >> > *Previous Position*
> >> > Ph.D Student,
> >> > Department of Biophysics, Molecular Biology and Bioinformatics,
> >> University
> >> > of Calcutta (CU), 92 APC Road, Kolkata - 700009, India. Phone:
> >> > +913323508386 (extn. 329, 321), Fax: +913323519755. Personal Mobile:
> >> > +919239202278
> >> > _______________________________________________
> >> > AMBER mailing list
> >> > AMBER.ambermd.org
> >> > http://lists.ambermd.org/mailman/listinfo/amber
> >>
> >>
> >>
> >> --
> >> -------------------------
> >> 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)
> >>
> >> _______________________________________________
> >> AMBER mailing list
> >> AMBER.ambermd.org
> >> http://lists.ambermd.org/mailman/listinfo/amber
> >>
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
>
>
>
> --
> -------------------------
> 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)
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Wed May 11 2016 - 10:30:02 PDT
