Re: [AMBER] solid surface interacting with organic

From: Jason Swails <>
Date: Fri, 19 Jun 2015 10:59:38 -0600

On Fri, Jun 19, 2015 at 4:12 AM, Azade Yazdan Yar <
> wrote:

> Dear all
> Hi
> 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
> advance.
> 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?

​You are venturing into territories largely untouched by most Amber
developers. We don't usually run simulations with surfaces (lipid bilayers
are close, but still markedly different). As a result, there really are no
tools in Amber that are designed to help you create starting structures
with surfaces. I would suggest using a different tool to create the
initial structure, and bring that to LEaP (note, each of the components in
your system requires a library matching atom names in the PDB file to atom
types and assigning charges -- you can use either an Amber OFF, mol2, or
Amber prep file for that purpose).

One comment is that Amber uses primarily an additive force field, which
means that you need parameters for each component, and they can all be
added together. So what you need are parameters for water, TiO2, and the
organic compound. Once you have those, the interactions between
water-TiO2, water-organic, and organic-TiO2​ are all defined automatically.

If you have the TiO2 and water parameters, all you need is the parameters
for the organic compound, which you can get using antechamber (see tutorial
B4 in You need to derive the force field
library and frcmod files for the organic compound. Then tleap should be
able to build the prmtop file for you.

Good luck!

Jason M. Swails
Rutgers University
Postdoctoral Researcher
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Received on Fri Jun 19 2015 - 10:00:02 PDT
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