[gmx-users] Water-Mediated Hydrogen Bonds
Justin A. Lemkul
jalemkul at vt.edu
Sat Jul 2 17:36:34 CEST 2011
Raja Pandian wrote:
> Dear Justin,
> Thanks for your mail.
> I don't have the programing knowledge.
It is exceptionally rare to find all of the software you already need in place
and freely available. You'd be well-advised to learn a language (or maybe even
a few) that suit your needs. For instance, Perl is handy for dealing with text
files in the way I suggested in the previous post.
> If it is possible, please send your program (water mediated hydrogen
> bond derivation program) to me and also the program operating procedure.
I don't have such a program. Perhaps someone else does.
> On Sat, Jul 2, 2011 at 5:24 PM, Justin A. Lemkul <jalemkul at vt.edu
> <mailto:jalemkul at vt.edu>> wrote:
> Raja Pandian wrote:
> Dear All,
> I’m doing research in the field of Protein-DNA interaction. I
> have gone through these papers,
> *A “Solvated Rotamer” Approach to Modeling Water-Mediated
> Hydrogen Bonds at Protein–Protein Interfaces*
> *“Effect on DNA relaxation of the single Thr718Ala mutation in
> human topoisomerase I: a functional and molecular dynamics study”*
> *“Molecular Dynamics Simulation Study of Interaction between
> Model Rough Hydrophobic Surfaces.”*
> *“Prediction of Protein Binding to DNA in the Presence of
> Water-Mediated Hydrogen Bonds”*
> I have found lot of interesting things on these papers that will
> be useful for the progress of my research carrier.
> I have been looking for water mediated hydrogen bond in my
> simulation when i use g_hbond the -ins option it dose not
> showing the water mediated hydrogen bond could you please tell
> me how to get the hydrogen mediated hydrogen bond and water
> mediated free energy in Gromacs ?
> Is there any way to calculate water mediated hydrogen bond
> between Protein-DNA using Gromacs tools?
> If it is possible, please send your program (water mediated
> hydrogen bond derivation program) to me and also the program
> operating procedure.
> This has been discussed several times in the list archive, for
> instance one solution is:
> Search "water mediated hydrogen bonds" and you will find many more
> posts about the same topic.
> Eagerly waiting for your reply.
> Thanking You
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080
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Justin A. Lemkul
ICTAS Doctoral Scholar
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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