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! -Sven 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 > > <https://www.linkedin.com/pub/sven-hackbusch/53/639/aa8> > > -- Sven Hackbusch PhD Candidate Department of Chemistry University of the Pacific <https://www.linkedin.com/pub/sven-hackbusch/53/639/aa8>