Re: Using CHARMM Compatible Amber Parameters

From: johan strumpfer (
Date: Wed Oct 19 2011 - 22:57:48 CDT


I'm not sure what the pref.dat file is for but hopefully this answers
your question: This is a pretty standard thing to do. You can use the
amber parameters in the non-charmm directory as found in
toppar_c35b2_c36a2.tgz, but you need to have
exclude scaled1-4
1-4scaling 0.833333
in the NAMD configuration file.


Johan Strumpfer:
Theoretical and Computational Biophysics Group
3115 Beckman Institute
University of Illinois at Urbana-Champaign
405 N. Mathews
Urbana, IL 61801, USA

On Wed, Oct 19, 2011 at 9:22 PM, Jernej Zidar <> wrote:
> Why don't you try using the CHARMM parameters for nucleic acids instead?
> "CHARMM-compatible Amber" parameters sounds like a bad idea to me.
> Regards,
> Jernej
> On 20. okt. 2011, at 09:10, Ehsan Ban wrote:
>> Hi Everyone,
>> I'm trying to use CHARMM compatible Amber parameters to simulate dsdna from:
>> Because Amber and CHARMM use different values to convert charge values to kcal/mol changes should be made to CHARMM program's pref.dat to work with these parameter files. Does anyone know how to get around this in NAMD?
>> Regards
>> Ehsan Ban
>> Rensselaer Polytechnic Institute

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