So far, you have explained how you calculated charges. Charge calculations
should not alter the 3D structure, so the procedure you outline would not
produce that geometry. At what specific step did the strange orientation
occur? Did you minimize the structure? If so, was it there before or
after minimization? If not, then what did you do? We need enough detail
for this to repeat exactly what you did, and this is not enough.
You say:
"i have created glucose structure and optimized the same in Gaussian with
b3lyp/6-31* method"
You created the entire 3D structure of the glucose there? That calculation
should not use any of the force field parameters. What was the structure
at the end of that calculation? Was the hydrogen already in that
orientation?
You say:
"I used simple glucose molecule because the parameter of glucose is already
available in amber."
Did you use the glycam06 parameters?
On Tue, Nov 21, 2017 at 11:48 PM, Aashish Bhatt <aashish.ph16221.inst.ac.in>
wrote:
> 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
> "*antechamber
> -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.
>
> Regards
> Aashish
>
>
> On Tue, Nov 21, 2017 at 7:26 PM, Lachele Foley <lf.list.gmail.com> 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 <
> aashish.ph16221.inst.ac.in
> > >
> > 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
> > > AMBER.ambermd.org
> > > http://lists.ambermd.org/mailman/listinfo/amber
> > >
> > >
> >
> >
> > --
> > :-) Lachele
> > Lachele Foley
> > CCRC/UGA
> > Athens, GA USA
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
:-) Lachele
Lachele Foley
CCRC/UGA
Athens, GA USA
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Received on Wed Nov 22 2017 - 07:30:03 PST
