Re: CMAP in NAMD simulation

From: Leonardo Trabuco (ltrabuco_at_ks.uiuc.edu)
Date: Sat Oct 14 2006 - 17:34:51 CDT

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Hi,

On Sat, Oct 14, 2006 at 03:26:23PM -0700, Neelanjana Sengupta wrote:
> Hello NAMD experts,
>
> The NAMD 2.6 manual says that " Both NAMD and psfgen (standalone or VMD
> plug) read and interpret the new CHARMM 31 stream files (combining topology
> and parameters) and the new CMAP crossterm (dihedral-dihedral) potential
> function."
>
> Could you tell me how I can implement CMAP can be implemented into a NAMD
> simulation of a protein or peptide? (ie. what is the format of input file,
> etc?)

If you use topology and parameter files with CMAP entries, it should
just work.

Best,
Leo

-- 
Leonardo Trabuco, Ph.D. student
Theoretical and Computational Biophysics Group
University of Illinois at Urbana-Champaign

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