Re: Using CHARMM Compatible Amber Parameters

From: johan strumpfer (johanstr_at_ks.uiuc.edu)
Date: Wed Oct 19 2011 - 22:57:48 CDT

Hi,

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.

Cheers,
Johan

------------------------------------------------------------------------------------------------------
Johan Strumpfer:         johanstr_at_ks.uiuc.edu        www.ks.uiuc.edu/~johanstr
Theoretical and Computational Biophysics Group
3115 Beckman Institute
University of Illinois at Urbana-Champaign
405 N. Mathews
Urbana, IL 61801, USA
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On Wed, Oct 19, 2011 at 9:22 PM, Jernej Zidar <jernej.zidar_at_gmail.com> 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:
>> http://www.chpc.utah.edu/~cheatham/software.html
>>
>> 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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