Re: [AMBER] Amber force field for PNIPAM

From: Vishal Maingi <>
Date: Fri, 3 Aug 2012 15:55:18 +0530

Dear Ganesh Kamath,

1) May be you can use strategy we used for building dendrimers. Though this
is hyperbranched polymer and PNIPAM is linear; but you can use methodology
to derive parameters (GAFF and RESP charges)

and once you have residues (with above method or your own) in your hand
then you may need starting coordinates for full polymer linear chain. You
can use DBT (dendrimer builder toolkit); which is integrated to AMBER
(which can help to get linear polymers also)

2) But I wonder if your polymer is not "turning" and just growing linear
and long then starting water box size will be huge to start with!! (some
one please chime in...). How many units you have in your polymer??

and finally

3) So you need three residues to build full polymer. Like this
{{As you must have also noticed, your poly has chiral center, so please
consider that also.}}

where A =

             || | \
            O H CH3

B =

             || | \
            O H CH3

C =

             || | \
            O H CH3

If you need more help how to use DBT please let me know. But you will have
to compare some property(ies) of PNIPAM to make sure whether derived
charges and parameters are reproducing experimental observations or not.


Vishal Maingi*
*Dendrimer Builder Toolkit (DBT)*
On Fri, Aug 3, 2012 at 5:06 AM, Ganesh Kamath <> wrote:
> Hi Folks,
>   I am trying to simulate a polymer of N-isopropyl acryl amide in water.
> Does any one have force field parameters in AMBER for this molecule.
> Can I use the LJ parameters and charges of NMA?
>                       CH3
>                       /
>              ||  |    \
>             O H    CH3
> Any help will be greatly appreciated.
> Thanks,
> ganesh
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Received on Fri Aug 03 2012 - 03:30:03 PDT
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