Thank you to everyone that has chimed in with your help!

I do have some follow-up questions about the MM energy minimization with
the targeted torsion restrained:

1. I assume that the minimizations are run in explicit solvent (TIP3P
model) - is this correct?
2. With what values do you restrain the torsion angle in your
minimizations? In my first attempt, I kept to the AMBER tutorial 4 by
setting r1 = angle - 2°, r2 = angle - 1°, r3 = angle + 1°, r4 = angle + 2°
 and rk2 = rk3 = 32.0, however this seems arbitrary to me and I did not
find anything given in the GLYCAM06 publication.

Thank you!

On Sun, Sep 18, 2016 at 3:43 PM, Rob Woods <[log in to unmask]> wrote:

> Hi Sven,
> To answer your specific question, yes, we normally would develop them
> using small representative training molecules. I would not expect there to
> be a torsion term required for the H2. My rule is that if it is small, it's
> preferable to use zero. But that is system dependent.
> Please remember to fit the charges with the aliphatic Hs constrained to
> have zero net charge.
> Good luck!
> Rob
> Excuse the brevity, sent from iPhone
> On Sep 18, 2016, at 11:50 AM, Xiaocong Wang <[log in to unmask] <[log in to unmask]>>
> wrote:
> Hi Sven,
> To develop torsion terms for missing terms in GLYCAM06, you will need to
> generate QM energy profile for that specific torsion.  To do that, optimize
> the molecule with that torsion restrained in QM (HF/6-31G*), then single
> point energy calculation with the optimized structure (B3LYP/6-31G*).  We
> usually vary the torsion angle every 30 degrees.
> Once we have QM optimized structures (targeted torsion restrained),
> perform MM energy minimization with targeted torsion restrained as well.
> For parameters you use in MM energy minimization, set V terms for that
> specific torsion to 0.  You will have the MM energies without rotational
> energy corrections ("torsion energies").  The differences between QM and MM
> (without rotational energy corrections) energies are what "torsion
> energies" are supposed to be.  Then, develop V terms to make sure
> rotational energies (sum from cosine functions) match the previous energy
> differences.
> It is not complicated, but it will take some time.  The logic behind
> torsion terms development is that torsion terms (rotational energies) are
> corrections in MM energy calculations.  Therefore, if the similar terms are
> fairly small, it means you could either copy from similar terms or set the
> V terms to 0.  Besides finding similar terms in GLYCAM06, you can also
> search similar ones in parm and gaff, which are available in AMBER.
> Best,
> Xiaocong Wang
> Complex Carbohydrate Research Center
> The University of Georgia
> 315 Riverbend Road,
> Athens, GA, 30602
> Tel: (706) 254-7958
> E-mail: [log in to unmask]
> ------------------------------
> *From:* Users of GLYCAM & GLYCAM-Web <[log in to unmask]
> <[log in to unmask]>> on behalf of Sven Hackbusch <
> [log in to unmask] <[log in to unmask]>>
> *Sent:* Friday, September 16, 2016 3:09:18 PM
> *To:* [log in to unmask] <[log in to unmask]>
> *Subject:* Re: GLYCAM parameters for 1-Acetylated sugars
> Hello Yohanna,
> Thank you for your offer to help!
> I think I will first try to use the approximation you recommend and
> compare the results to QM computations to verify it is a good enough
> approximation.
> If I understand the Glycam06 paper correctly, I will need to generate a
> rotational energy curve for the rotation about the Cg-Os bond for my
> molecule at the B3LYP/6-31++G(2d,2p)//HF/6-31G* level of theory and then
> to compare this curve to the GLYCAM06 result.
> --Can you explain how I generate the rotational energy curve from the
> GLYCAM06 parameters?
> If I were to have to develop my own parameters, would it be correct to use
> two simple compounds (methyl methoxyacetate and tetrahydro-2H-pyran-2-yl
> acetate) as a training set to generate the parameters?
> Here, I am not completely clear on how the fitting of the parameter terms
> was performed (in terms of the math involved) and how the rotational energy
> curve was divided into the respective atomic sequences (as opposed to using
> just a single atomic sequence in GLYCAM93).
> Thank you again!
>   -Sven
> On Fri, Sep 16, 2016 at 7:17 AM, Yohanna White <[log in to unmask]>
> wrote:
>> Hello Sven,
>> You have several options for this case. You can either make
>> approximations and make a guess on the torsion terms, develop your own
>> parameters, or we can develop the parameters for you and guide you through
>> it (but this will take us about 6 weeks to get to).
>> So if you'd like to make some approximations, you could set  the
>> Os-Cg-Os-C to the same term as a Cg-Cg-Os-C, assuming that if this were a
>> hexane, its torsion term would be similar. And you can set the H2-Cg-Os-C
>> to 0 so it won't have a torsion term.
>> Let us know if which plan works best for you.
>> Thanks,
>> Yohanna
>> On Tue, Sep 13, 2016 at 9:30 PM, Sven Hackbusch <
>> [log in to unmask]> wrote:
>>> Dear GLYCAM developers and users,
>>> I am interested in simulating a sugar that is acetylated at the 1
>>> position, specifically 1,6-Ac2-alpha-D-Glc, with the GLYCAM forcefield in
>>> Amber.
>>> It would appear that there exist no partial charges for this compound
>>> (the online builder did not let me place an acetyl derivative at position
>>> 1), so I am using the general protocol for deriving the partial charges.
>>> However, in generating the prmtop file using xleap I am encountering the
>>> following errors:
>>>  ** No torsion terms for Os-Cg-Os-C
>>>  ** No torsion terms for H2-Cg-Os-C
>>> Presumably, GLYCAM is missing the dihedral angle parameters for the
>>> O5-C1-O1-C(acetyl) and H1-C1-O1-C(acetyl) dihedral angles.
>>> Can anyone advise a way to overcome this roadblock?
>>> Thank you very much for your help!
>>>   -Sven
>>> --
>>> Sven Hackbusch
>>> PhD Candidate
>>> Department of Chemistry
>>> University of the Pacific
> --
> Sven Hackbusch
> PhD Candidate
> Department of Chemistry
> University of the Pacific
>  <>


Sven Hackbusch
PhD Candidate
Department of Chemistry
University of the Pacific