It sounds to me like the analysis you want to do is to calculate a radial
distribution function in ptraj (which will effectively give you a graph of
how many solvent molecules are present as a function of distance from a
given solute mask). This is described in the manual via the "radial"
command.
If you integrate the RDF from 0 to whichever distance you want, that should
give you the number of water molecules within that distance cutoff of the
Zn ion (something that xmgrace does very easily under
Data->Transformations->Integration).
Related commands to your request is a distance-based cutoff mask, but I
don't think that selection is updated each frame, so only the first frame
will be correct if you use that (in conjunction with "strip", or something
similar). You can also use the "closest" command, but that will make you
specify how many atoms you want to keep, and it will just keep that number
that are closest to the given mask.
HTH,
Jason
On Sat, Jan 14, 2012 at 2:57 AM, kanika singal <singalkanika1.gmail.com>wrote:
> Dear AmberUsers,
>
> I am doing a metal protein simulation. I want to calculate the number of
> water molecules present within a distance cutoff of the Zn ion. I guess for
> this i should use hbond analysis from ptraj. However, in hbond analysis,
> the acceptor mask requires a heavy atom and a hydrogen atom. In my case,
> the Zn ion does not have a hydrogen bonded to it and as a result ptraj is
> showing error with the mask. How do I specify the details. I have seen a
> lot of papers, wherein one calculates the water molecules ard the metal
> ion. How are such calculations done??
>
> Should i consider the metal ion as a donor. Would that be wrong.
>
> Any help would be highly appreciated.
>
> Thanks & Regards,
> Kanika
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>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Sat Jan 14 2012 - 07:00:04 PST
