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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 >> > >