RE: Missing atom type for hydroperoxide

From: Radak, Brian K (
Date: Tue Jun 14 2016 - 12:58:25 CDT

This seems like a question for the CHARMM force field developers - I don't know how many of them actually frequent this list.

My (limited!) knowledge of the force field would lead me to guess that such a modification does not exist at present. It might be possible to use CGenFF on a peroxide fragment and then graft a patch onto the phosphate: 1.) I have no idea if that is an at all recommended procedure and 2.) my experience with phosphate force fields says that will almost certainly not lead to ideal parameters.


Brian Radak
Postdoctoral Appointee
Leadership Computing Facility
Argonne National Laboratory

9700 South Cass Avenue, Bldg. 240
Argonne, IL 60439-4854
(630) 252-8643
From: [] on behalf of Jean-François Fabre []
Sent: Tuesday, June 14, 2016 10:48 AM
Subject: namd-l: Missing atom type for hydroperoxide

Dear all,

I try to perform a simulation of an oxidized phospholipid with a hydroperoxide -OOH. I have to use CHARMM forcefield to compare with other molecules but it does not recognize the atom type of the oxygen -OOH. Is there a simple way to parametrize the forcefield to simulate this molecule or do I have to change the forcefield.

Thank you for your answer !


Jean-François Fabre

Jean-François Fabre
Ingénieur d'études
Laboratoire de Chimie Agro-Industrielle (LCAI) UMR 1010 INRA-INPT/ENSIACET
4 allée Emile Monso
31030 Toulouse cedex 4
Tél: 05 34 32 35 25

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