AMBER Archive (2007)

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

From: sanket deshmukh (sanket.deshmukh_at_ucd.ie)
Date: Thu Nov 08 2007 - 13:29:35 CST

Hi,
Thanks for your suggestions David. I created a pdb file without any
united atom in it (attaching it with this email) but still I am facing
the same problem. Antechamber can't find the connectivity properly. I
am just wondering do I have to use 'TER' or 'END' characters in my pdb
to direct the antechamber to read the pdb correctly? I am new to Amber
so please bear with me. Another thing I would like to know is about
preparing the prep file directly rather than using antechamber. Is it
correct to do that?

Any suggestion is appreciated.
Thanks in advance!
Sanket

----- Original Message -----
From: "David A. Case" <case_at_scripps.edu>
Date: Wednesday, October 31, 2007 9:58 pm
Subject: Re: AMBER: Amber 9: Generating Input files for EVB simulations
of the crosslinked structures (Hydrogels)
To: amber_at_scripps.edu

> 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.
>
> ....regards...dac
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