[AMBER] solid surface interacting with organic

From: Azade Yazdan Yar <azade.yazdanyar.gmail.com>
Date: Fri, 19 Jun 2015 12:12:55 +0200

Dear all

I am very new to Amber and trying to understand how it works by reading the
manual and going through some tutorials. However, I am not sure where to
start for what I want to do. Hope you can give me some hints. Thanks in

I want to study the interaction of an organic species (simple to
complicated, e.g. an amino acid or a polypeptide) with TiO2 surface
solvated in water. What I need, to do this, is the force field and the
interaction between different parts of my system. I already have the
water-TiO2 force filed. I need organic-water and organic-TiO2 force fields.
I assume what I have to do it to build the TiO2-water-organic system and
then get the force filed (is there any other way?). But I do not know how
to do this! Can I use tleap/xleap for this? and for generating the force
filed, what amber tool should I use?

Any suggestion is highly appreciated. Please let me know if I have to
follow another path rather what I explained.

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Received on Fri Jun 19 2015 - 03:30:03 PDT
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