Re: [AMBER] protein+DNA simulation

From: Dean Cuebas <>
Date: Thu, 23 Aug 2012 11:50:45 -0500

My first question would be why do you NOT want to use the crystallographic

If you are searching for other possible modes of binding, you definitely
need a docking program first. Use VINA, from the people who made Autodock.
It is lightning fast and the genetic algorithms are good enough to allow
you to simply place the ligand in the same "box" as the receptor and
attempt a "blind" docking, or, you can place the ligand at specific places
that you "think" it should bind.

Both apps are free. Just be sure to read ALL the documentation setting up
your system. Be aware that VINA and Autodock use a united atom approach,
only polar and aromatic hydrogens are used, so after you obtain the best
docking poses, don't forget that you need to add all the other hydrogens.
For proteins, I use the H++ and Molprobity servers.

The reason the docking programs are so fast, is that the conformations of
the ligand and receptors are for the most part frozen. Autodock/VINA
allows you to make some selections of "flexible" bonds for rotations in
both the ligand and the receptor, but you must minimize how many you use
or else your conformational possibilities skyrockets and your docking will
take forever. Conversely, you need to consider that if you don't allow
some bonds to rotate, you might not get the docking that is possible
because you've restricted the conformation of the structures. But since
your ligand and receptors are large biomolecules, it becomes very
difficult to decide what bonds to allow to rotate at all!

Hope this helps,

Dr. Dean Cuebas, Associate Prof of Chemistry, Ph 417-836-8567 FAX 417-836-5507
Dept. of Chemistry, Missouri State University
Springfield, Missouri 65897

On 8/22/12 1:40 PM, "najmul arfin" <> wrote:

>dear users,
>i am trying md simulation for dna+protein system ...but i don't want
>to take combined crystallographic structure from pdb bank.
>My problem is that if i take separate structure of protein and and
>separate DNA structure from pdb bank and merge it in common pdb file
>...then how i will ensure that after minimization and long md run,
>protein will go and attach to DNA with lowest free energy ...because
>it can get trap to any random position with not the lowest possible
>Moreover, placing protein close to DNA and then after MD checking free
>energy is not feasible , as i need to search for as many orientation
>of protein near DNA for best feasible protein-DNA structure.
> I was thinking of doing it with ROSETTA , but is there any better
>option in AMBER or any software.
> yours suggestions will be valuable to me.
>-- Regards
>Research Scholar
>NEW DELHI -110067
>AMBER mailing list

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Received on Thu Aug 23 2012 - 10:00:17 PDT
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