[AMBER] Help with Missing Torsion Parameters for TCO and TCNitro FRET Probes in DNA System

Contemporary messages sorted: [ by date ] [ by thread ] [ by subject ] [ by author ] [ by messages with attachments ]

From: Rahul Singal via AMBER <amber.ambermd.org>
Date: Sun, 30 Mar 2025 17:32:44 +0000

Hi AMBER Community,
I am currently modeling a DNA system incorporating TCO and TCNitro FRET probes. I initially used Antechamber to generate the parameters for the probes, but I recently realized that I should have used parmcal to compute the bond and angle parameters using GAFF2 (as provided in the gaff2.dat file in AmberTools23).
While I was able to calculate most parameters, I couldn't find the torsion parameters for the following dihedrals:

  *
h1–c3–o–P
  *
c3–c3–o–P
  *
c3–o–P–O2
  *
c3–o–P–OS

I would greatly appreciate any guidance on how to obtain or derive these missing torsion parameters.
Thank you in advance for your help!
Best regards,
Rahul Singal
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Sun Mar 30 2025 - 11:00:02 PDT