Re: [AMBER] Query about the Glucose Parameters

From: Aashish Bhatt <>
Date: Wed, 22 Nov 2017 10:18:15 +0530

Dear Sir/Ma'am

I need to specify that i have executed this calculation for better
understanding of force field. So I used simple glucose molecule because the
parameter of glucose is already available in amber.
In the next step, i have created glucose structure and optimized the same
in Gaussian with b3lyp/6-31* method. After optimization, i have calculated
the ESP charge from #P HF/6-31G* SCF=Tight Pop=MK
IOp(6/33=2,6/41=10,6/42=17) method. I have used resp charge by the
-i quer.log -fi gout -o quer.mol2 -fo mol2 -c resp" *command. Afterwards i
prepared the .lib file and then made topology and coordinate file.


On Tue, Nov 21, 2017 at 7:26 PM, Lachele Foley <> wrote:

> 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
> system.
> 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 <
> >
> wrote:
> > 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
AMBER mailing list
Received on Tue Nov 21 2017 - 21:00:04 PST
Custom Search