Re: parameters for NAD,NAG,NAP

From: Aaron Oakley (oakley_at_rsc.anu.edu.au)
Date: Thu Feb 03 2005 - 21:14:14 CST

Are these substrates/products?

The carbohydrate solution force field CSFF
is available for sugars, but not N-acetyl Glucosamine
(assuming this is what NAG refers to).

You might have to do some parameter development.

On 03/02/2005, at 8:39 PM, bora erdemli wrote:

> Hi,
>
> Basically I have two questions;
>
> 1) I am going to simulate protein complexes which have
> the following hetero groups NAD,NAG and NAP. What if I
> simulate only the protein complexes by extracting from
> PDB file without heterogroups? Does it have an effect
> which alters the physical results of my simulation?
>
> 2)If I have to do the simulation together with the
> hjeterogroups, I need parameter and topology files
> which include parameters for these groups. Previously,
> I use param27 and topol27 files but they only contains
> infromation for NAD but not the others. Does anybody
> have releavent information about the parameters that I
> need?
>
>
> sincerely yours
>
>
>
>
>
> =====
> Sabri Bora Erdemli
> Koc University
> Computational Science and Engineering
> Research and Teaching Asistant
> Koc Universitesi pk.218 34550
> sariyer Istanbul/TURKEY
> tel no: 02123381736
> 05326512523
>
>
>
>
>
>
>
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