Re: AMBER: Amber 9: Generating Input files for EVB simulations of the crosslinked structures (Hydrogels)

From: David A. Case <>
Date: Wed, 31 Oct 2007 14:52:18 -0700

On Wed, Oct 31, 2007, sanket deshmukh wrote:

> I want to run EVB simulation of the hydrogel structure (basically a
> crosslinked structure) of a poly(methacrylic acid) in presence of water.

> It is a united atom structure (I am attaching a pdb file with this
> mail). I have a pdb file generated from my program. I tried to use
> antechamber but it is not recognising the connectivity (though I am
> giving the ?CONNECT? list in the pdb)

Antechamber does not know about united atom force fields, and does not use the
CONECT records in any event. If you are sure that you want a united atom
force field, you will have to generate the needed parameters by hand.

> 1. Is it possible to run EVB for such a system?

EVB should work -- I am assuming that you know what V11 and V22 should be in
your example. EVB is designed for the simple description of reactive events;
if that applies to you, and if you understand the ideas behind EVB, then you
should be able to proceed.

> 3. When I tried to generate the prep file for the structure, I tried to
> use united atom force field. I got confused as my structure has some
> bonds like C-O-CH2 (C-O-C2 according to the Amber nomenclature) which
> this force field doesn?t explain. So what can I do in such cases?

You will have to develop united atom ether parameters on your own: you might
study the way in which the protein united atom parameters were developed, and
follow that.

However, are you *sure* you need a united atom calculation? The water
molecules will all have hydrogens, so leaving them out of the solute might not
save all that much effort. There are fairly good reasons why united atom
force fields are not used much anymore -- be sure you understand that pros and
cons (mostly cons, in my view) of this choice.

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Received on Sun Nov 04 2007 - 06:07:15 PST
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