Re: [AMBER] Nuclicacid forcefield in AMBER

From: Nhai <>
Date: Wed, 18 Mar 2015 11:20:35 -0400

The newly updated gbneck2 for nuc will be available in sander in new Ambertools (version 15, next few months).


> On Mar 18, 2015, at 8:01 AM, Carlos Simmerling <> wrote:
> We are just finishing parameters for nucleic acids in our GBneck2 implicit
> solvent model. If you can't get your GROMOS option to work, this may be
> worth a try. So far we have only looked at structural properties using the
> GB model and not compared thermodynamics to experiment, so you would have
> to carefully check your results.
>> On Tue, Mar 17, 2015 at 12:27 PM, mish <> wrote:
>> Many thanks. I also feel that nucleobase-protein thermodynamics using
>> implicit solvent models may not be a good way to start. I will have a look
>> if GROMOS force field can be imported in AMBER somehow.
>> Many thanks,
>> Mish
>> On Mon, Mar 16, 2015 at 1:33 AM, David A Case <>
>> wrote:
>>>> On Sun, Mar 15, 2015, mish wrote:
>>>> I would like to know about some appropriate force-field in AMBER to
>> play
>>>> with the thermodynamics of nucleobases binding to proteins? I am very
>> new
>>>> to simulations of nucleic acids, so have not much idea, which ff to
>> start
>>>> with. There are many articles using certain versions of GROMOS, but I
>> am
>>>> not aware of such developments after AMBER-99 in AMBER community. If
>>> there
>>>> are some advanced ff that can be used for simulation of single
>> nucleobase
>>>> binding to proteins using implicit solvent models?
>>> You could first create units that just have the nucleobase. I'd suggest
>>> starting with the nucleosides, removing the sugar part that you don't
>>> want, and capping the N1 or N9 position with a methyl or whatever group
>>> matches the experimental situation you with to simulate. If you started
>>> from ff14SB, you would then have a nucleobase parameterized in way that
>> is
>>> consistent with the way proteins are parameterized.
>>> Of course, if you know that GROMOS force fields have been specifically
>>> tested for this sort of interaction, you may wish to follow that lead. A
>>> lot depends on what you wish to do with the results. Don't expect great
>>> accuracy for nucleobase-protein thermodynamics using implicit solvent
>>> models, but poses (geometries) might be of use.
>>> ...good luck....dac
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Received on Wed Mar 18 2015 - 08:30:05 PDT
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