Re: [AMBER] RESP charges for a peptide-bound probe with R.E.D.

From: Andrew Schaub <>
Date: Mon, 16 Oct 2017 17:15:44 -0700

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,


On Mon, Oct 16, 2017 at 4:00 PM, Seth Axen <> 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?
> _______________________________________________
> AMBER mailing list

Andrew Schaub
Graduate Program in Chemical & Structural Biology
Tsai Lab, http:/// <>
Luo Lab,
University of California, Irvine
Irvine, CA 92697-2280
949-824-8829 (lab)
949-877-9380 (cell)  <>
AMBER mailing list
Received on Mon Oct 16 2017 - 17:30:01 PDT
Custom Search