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

From: sanket deshmukh <>
Date: Wed, 31 Oct 2007 18:57:54 +0000 (GMT)

Dear All,
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) and because of that it is failing.
 So I decided to generate .prep file by modifying the code rather than
using the antechamber. So my questions are:

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

2. As antechamber is not working properly with this structure, is it
correct to generate a prep file by using the parameters from the force

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?

4. How can I calculate the charges in this case? I am planning to use
hyperchem to do so, can I use it?

5. Can I use GAFF rather than united atom force field? If I am using
GAFF can I use the parameters of GROMOS-96 force field?

(Note: I am attaching two pdb files for differet different hydrogels
1. christc1.pdb: In this all the crosslinkers (BIS) are connected with
the monomer (n,n’ isopropyl acrylamide) chains i.e. the structure is
saturated. 2. METACR.pdb: In this the structure the crosslinker (GLY)
is not fully connected (it has some ends with CH at the end) but this
structure will do for me. I can generate the saturated structure for 2
but at the moment getting started is important for me.)

Thanks in Advance!

Sanket A Deshmukh
Research Student
School of Chemical and Bioprocess Engineering,
Engineering and Material Science Building,
University College Dublin,
Dublin-04, Ireland.
Mob. +353 862132132.
Off. +353 17061866.

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Received on Sun Nov 04 2007 - 06:07:13 PST
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