[gmx-users] Simulating multiple fragments

R.S.K.Vijayan biovijayan at gmail.com
Sat Jan 14 21:00:33 CET 2012

Hi all

I was wondering if some body has done simulating multiple copies  of small
lead like fragments in a solvated box .

I want to soak my proteins with  multiple copies of diverse fragments along
with water as iam interested in finding  the hot spots in proteins that can
be  successfully employed for fragment based drug design. The approach  is
 analogs to the MCSS approach developed by Prof Karplus and the recent
SILCS approach by Prof Mackerell.

The impediments which i theoretically fore see are
1) how to negate interactions terms between two fragments as
two fragments may be competing for the same site.
2) How to create multiple topologies for multiple copies of the
same fragment randomly placed all over the fragment
3) Iam also skeptical whether the  fragments will be able to find their
respective binding site  in a nanosecond  time scale  when started De Novo
 contrary to the well settled proposition of docking
and keeping the fragment in the active site. A look at this paper by DE
Shaw  " How Does a Drug Molecule Find Its Target Binding Site??" reveals
the binding event to be captured on a mili second time second.

Thanking you in advance for all thought provoking suggestions.


On Sat, Jan 14, 2012 at 10:45 PM, Justin A. Lemkul <jalemkul at vt.edu> wrote:

> Hovakim Grabski wrote:
>> Hi,
>> Anyone know any ligand- ligand tutorial?
> If there is no receptor, then there is no ligand ;)
>  I've been trying to set up a taurine  simulation with
>> lysophosphatidylcholines (LPC) with no success.
> Without a description of what you've tried, what hasn't worked, etc then
> there's not much anyone can suggest.  If you've simply got two small
> molecules you want to simulate together:
> 1. Obtain topologies for both species and construct a .top that calls a
> force field and the small molecule topologies
> 2. Set up the coordinate file such that the two species are arranged how
> you'd like them in a single box (done with editconf)
> 3. Solvate and proceed as you would any other simulated system
> -Justin
> --
> ==============================**==========
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
> ==============================**==========
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