Print

Print


Hi Oliver and Xiaocong,

I understand your point, and it does seem to be a right choice to handle my
systems. I am basically dealing with UDP-GlcNAc and some glycans attached
to the Ribitol phosphates. Thus, parameters would be crucial in this case.
I don't think there is any easy workaround, instead parameterizing them
(which also needs to be validated first).

Many thanks,
Sushil


On Thu, Dec 15, 2016 at 10:00 PM, Xiaocong Wang <[log in to unmask]> wrote:

> I agree with Oliver.  We do this when the connection part is not important
> for the essential properties of the molecule that you are modeling.  You
> can also check out the supplemental material of the following paper:
> http://www.nature.com/articles/ncomms7387
>
> I used parm for amino acid, but GLYCAM for sulfate.
>
> Good luck!
>
> Xiao
>
>
> 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]> on
> behalf of Oliver Grant <[log in to unmask]>
> *Sent:* Wednesday, December 14, 2016 10:26:29 AM
> *To:* [log in to unmask]
> *Subject:* Re: About using GLYCAM and GAFF for a molecule
>
> Hi Sushil,
>
> You can do this, but I wouldn't trust it for something that needs to be
> high accuracy and/or can't be validated. I did it for modeling linkers
> attached to glycans here https://www.ncbi.nlm.nih.
> gov/pmc/articles/PMC3854501/, where it didn't matter about getting
> populations of rotamers correct, or if some of the shapes produced weren't
> populated in reality.
>
> See attached frcmod file for what we did. There is a note with each
> parameter explaining where I took it from. Sp8, Sp10 etc refer to linkers
> (spacers) on the consortium for functional glycomics (CFG) glycan arrays.
> Check Table 1 in the publication for the molecular structures of the
> linkers.
>
> Oliver
>
> On Sat, Dec 10, 2016 at 9:04 AM, Sushil Mishra <[log in to unmask]>
> wrote:
>
>> Hi,
>>
>> I do not have particular specific case but rather a general question
>> about using GLYCAM and GAFF together. I am frequently seeing some
>> ligands, which have a glyacn attached to it (e.g. UDP-GlcNAc,
>> dTDP-Rhanmonse, heparin sulphate etc). I wonder if there is an easy
>> workaround to use GLYCAM for glycan part of the ligand and GAFF for rest of
>> the molecule.
>>
>> What I was thinking as of now is generate GAFF parameters for the whole
>> molecule and later renaming glycan part (atom names and residue name) to
>> GLYCAM. Missing parameters can be be generated in frcmod file (using
>> parmchk ) ? What I may be missing is parameters for the "connecting bond,
>> angle, dihedral etc".
>>
>>
>> Have someone tried such a case and can suggest me something ?
>>
>> Best,
>> Sushil
>>
>
>