Sir,
ok sir. Thank u very much for the reply.
i have tried dock 6.5 for docking the molecule into the dna. i tried
autodock also. they give entirely diffrerent result. auto dock doesnt
consider hydrogen atoms of the ligand for deriving the best docked state as
i understand. so i go with dock. sir, what do you mean by different
parameterization of the ligand force field. i have used hf/6-31g* for
gaussian and leaprc.gaff for use in leap.
In fact preparing input in leap all go success. so should i conclude
initial docked conformation choosed may be the problem.
Thanking you
Mary Varughese
On Thu, May 9, 2013 at 6:33 PM, David A Case <case.biomaps.rutgers.edu>wrote:
> On Thu, May 09, 2013, Mary Varughese wrote:
>
> > But after a 4-5ns, the ligand strats unbinding and later completely
> > withdrawn from the dna.
>
> >From your mail, there is no real evidence that this is an incorrect
> result.
> It is not uncommon to see things like this. You probably need to examine
> different starting configuations, maybe different parameterization of the
> ligand force field; maybe just recognize that biomolecular simualtions are
> far
> from perfect.
>
> Of course, there could be errors in your input or in the programs
> themselves,
> but it generally takes a lot of experimentation and debugging to find
> these.
>
> ....dac
>
>
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Received on Thu May 09 2013 - 07:00:05 PDT
