Thanks, Andrew! I really appreciate the feedback and advice.
Seth
On Mon, Oct 16, 2017 at 5:15 PM, Andrew Schaub <aschaub.uci.edu> wrote:
> Hey Seth,
>
> Your fragmentation strategy looks good to me. It would be nice if they
> could be smaller as it would speed up computation time, but with those
> aromatic moieties I think this is as small as you can get away, as the
> point of the cap is to mimic the neighboring chemical environment. Yeh
> R.E.D. will use parameters from parm10.dat when possible. Pay close
> attention to the atom types assigned, and verify that they make sense. For
> example, atom type CT is an sp3 carbon (generic), but CX is an sp3 carbon
> that functions as an alpha-carbon. If needed, you can create new atom
> types. The other parameters (torsions, etc.) will have to be added. Your
> best bet would be to use Paramfit.
>
> Best Regards,
>
> Andrew
>
> On Mon, Oct 16, 2017 at 4:00 PM, Seth Axen <seth.axen.gmail.com> wrote:
>
> > This question is regarding the R.E.D. server and has been posted on the
> > q4md mailing list, but I am also posting it here to solicit expert
> advice.
> > I am endeavoring to derive RESP charges for a fluorescent probe/dye
> > covalently bound to either a cysteine or a lysine, each with its own
> linker
> > (see attached schema.gif). After reading through the R.E.D. tutorial and
> a
> > number of R.E.DD.B. projects, I have developed the following proposed
> > approach (see attached schema):
> >
> > Using a fragment-based approach, I divide each target molecule into three
> > fragments (dipeptide, linker, probe), where the probe is common for both
> > molecules. Rather than take existing Cys and Lys charges, I re-fit them
> > using a dipeptide and capping groups. Suitable capping groups are
> selected
> > for each fragment, and intra- and inter-molecular charge constraints are
> > used. Due to the inherent symmetry in the probe and its preference for
> > planarity, I consider it as a single fragment with charge +1 and only one
> > conformer.
> >
> > How do this fragment approach and the corresponding capping groups look?
> > Should the probe be separated into smaller fragments? To generate the
> > entire molecule, should each assembled molecule of interest
> > (dipeptide-linker-probe) also be included in the optimization? Lastly, it
> > is my understanding that R.E.D. does not derive missing angle and torsion
> > parameters but relies on the user to provide them by analogy. Is
> > antechamber the best approach for obtaining these analogies if none can
> be
> > found in the literature?
> >
> > _______________________________________________
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> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
> >
>
>
> --
> Andrew Schaub
> Graduate Program in Chemical & Structural Biology
> Tsai Lab, http:///www.tsailabuci.com/ <http://www.tsailabuci.com/>
> Luo Lab, http://rayl0.bio.uci.edu/html/
> University of California, Irvine
> Irvine, CA 92697-2280
> 949-824-8829 (lab)
> 949-877-9380 (cell)
> aschaub.uci.edu <http://www.linkedin.com/pub/andrew-schaub/9a/907/382/>
> _______________________________________________
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>
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Received on Tue Oct 17 2017 - 09:00:03 PDT
