Re: [AMBER] Query about the Glucose Parameters

From: Lachele Foley <>
Date: Tue, 21 Nov 2017 08:56:16 -0500

You will definitely get different charges if you do different types of
calculations to obtain them. There are no 'correct' charges. In physical
actuality, partial charges do not exist at all. The ones that were
developed for GLYCAM06 were developed to work with the rest of the force
field. If you change those charges, it's hard to say what sort of results
you will get. If you get bad results, then either your charges are not
good or there is some other problem with the way you're setting up the

Why are you making a lib file for GLC? You can make a topology and inpcrd
file for glucose using the method described in the earlier thread. Why not
just use that method? Are you doing that just so you can change the
charges? If so, then just make alternate versions of the prep files with
your different charges. Doing that eliminates one source of possible error.

If the anomeric OH binds to the O5, then there is something wrong with the
set of parameters you have constructed. Why not use the ones that already
exist? What do you want to do that makes you want to use Gaussian and
calculate new charges?

In any case, if you observe unusual behavior, we need to know exactly what
you did before we can help. We need a lot more information than what you
have given us.

On Mon, Nov 20, 2017 at 7:00 AM, Aashish Bhatt <>

> Dear Sir/ Ma'am
> I am facing a problem in 0GA+ROH carbohydrate parameter while doing force
> field preparation for glucose molecule. I have used Gaussian optimized
> structure and calculated the MK charges(Gaussian) and resp
> charges(antechamber). Then I compared the results with 0GA+ROH.dat file and
> found differences between the two. I have created the library file resp.lib
> and mk.lib for preparation of topology and coordinate file for Glucose
> molecule. I observed that the anomeric OH binds to the O5 atom of Glucose
> in both vacuum and solvated phase. I don't know the reason behind this
> unusual binding behavior. Kindly help me if there is any charge related
> issue of atoms in library file.
> I am attaching both the library files along with 0GA+ROH.dat.
> Thanking You
> In wait of your kind reply.
> With regards
> Aashish
> _______________________________________________
> AMBER mailing list

:-) Lachele
Lachele Foley
Athens, GA USA
AMBER mailing list
Received on Tue Nov 21 2017 - 06:00:04 PST
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