Actually in this paper *
http://pubs.acs.org/doi/abs/10.1021/jp0468657?journalCode=jpcbfk&quickLinkVolume=109&quickLinkPage=11046&selectedTab=citation&volume=109
* ,
they have analysed sugar clusters using some hydrogen bond criterion .
i am interested in doing this kind of analysis.
thanking you
subrata
On Tue, Sep 24, 2013 at 1:53 PM, Karl N. Kirschner <
kkirsch.scai.fraunhofer.de> wrote:
> Hello Subrata,
>
> I think I understand what you want to do, but let me paraphrase it for
> clarity. You are looking at pure water cluster with the goal of
> understanding what type of 3D hydrogen bonded motifs are formed (e.g.
> prisms, books, cubes of pentamers, octamers, dodecahedrons). I have also
> used MD simulations to do this, but have not come up with a methodology to
> do automatic clustering to identify unique motifs. I believe the problem is
> that the adopted structure of the system is dependent upon the nonbonded
> forces - meaning that the each waters drastically changes its hydrogen bond
> partners (and loacation) during the trajectory course. This makes doing an
> RMSD for such a system, using AmberTools, tough since it is dependent upon
> the residue names. For biological molecules this is not a problem since
> they are covalently bonded structures and neighboring residues do not
> change their partners and their secondary structure is relatively stable
> (compared to water clusters structures). Our solution has been to extract X
> number of trajectory snapshots and perform some QM calculations on them;
> subsequently their structures were manually evaluated to remove redundant
> motifs. Here are a couple of articles that illustrate this process:
>
> http://dx.doi.org/10.1016/j.comptc.2013.07.039
> http://pubs.acs.org/doi/abs/10.1021/jp2119026
>
> Best regards,
> Karl
>
> ----- Original Message -----
> From: "Subrata Paul" <paul.subrata34.gmail.com>
> To: "AMBER Mailing List" <amber.ambermd.org>
> Sent: Tuesday, September 24, 2013 6:30:44 AM
> Subject: Re: [AMBER] water cluster analysis
>
> Dear Jason
>
> Actually, I want to calculate hydrogen bonded water cluster.
>
> and how many such kind of water cluster are there.
> Is it possible ? any software ?
>
>
> --
> *With Best Regards
> Subrata
> PhD Student
> Dept of Chemistry.
> IIT G
> *
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--
*With Best Regards
Subrata
PhD Student
Dept of Chemistry.
IIT G
*
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Received on Tue Sep 24 2013 - 02:00:04 PDT
