[AMBER] Advice on applying restraints

From: Matthew Guberman-Pfeffer via AMBER <amber.ambermd.org>
Date: Sat, 16 Jul 2022 15:48:01 -0400

Dear Amber Community,

Background: I have a disordered protein with a missing loop. I added the loop, and it connects well to the rest of the protein after minimization. But, between the added loop and the rest of the protein there is a “pore” and I’m not sure if the loop should be packed into that pore. I want to see if I can at least close the gap somewhat.

Attempt #1: I defined a moving restraint (centered at 22 Å and goes to 7 Å) between the alpha carbons of the added loop and an alpha carbon of a residue on the other side of the “pore.” This simulation runs fine, except the entire structure distorts at the loop is pulled in.

Attempt #2: I kept the moving restraint, but added positional restraints to the rest of the backbone. This simulation fails after ~4 steps with NaN energies.

Question: Any thoughts on what I could try next to bring the two parts of the protein closer together so there is not a gaping whole.


AMBER mailing list
Received on Thu Aug 04 2022 - 13:34:27 PDT
Custom Search