[AMBER] Repulsive restraints between two atoms or two groups of atoms

From: Antonio Frances Monerris via AMBER <amber.ambermd.org>
Date: Tue, 04 Apr 2023 13:33:14 +0200

Dear Amber community,

I am interested in running simulations of a DNA double strand and some small drugs. I want to avoid favorable interactions of the drug with the DNA terminal base pairs, which have no biological meaning. Therefore, one possibility is to add repulsive potentials between these fragments and the drug, which are only active at short DNA termninal/drug distances.

I could not find much information about adding repulsive potentials in Amber on the internet. I just found in an old Amber post the possibility to include negative force constants for an harmonic potential, in the form:

 &rst
  iat=1291,20,
  r1=0.0,r2=13.0,r3=13.00,r4=20.0,
  rk2=-65.0, rk3=0.0,
/


This would add a repulsion between atoms 1291 and 20 with a force constant of -65 kcal/mol in distances between 0 and 13 Angstrom, and of 0 kcal/mol at distances between 13 and 20 Angstrom.

However, this strategy is not working well. In some instances, instead of repulsion, the atoms are approaching each other blowing up the simulation.

Am I doing it correctly? Is there any other possibility to avoid these undesired contacts?

Thanks for your time.

Best regards,
Antonio

-- 
********************************************
Dr. Antonio Francés Monerris
Assistant Professor
Institut de Ciència Molecular (ICMol) &
Departament de Química Física
Universitat de València
Phone: +34 963544404
E-mail: antonio.frances.uv.es
********************************************
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Received on Tue Apr 04 2023 - 05:00:02 PDT