Re: ATP and Stream files

From: Dimitar V Pachov (
Date: Thu Oct 15 2009 - 08:55:02 CDT

This file also contains the parameters for ATP, so you have to have two "parameters" statement in your configuration file every time you use ATP in your simulations - one containing general force field parameters and the other appending the parameters for ATP (toppar_all27_na_nad_ppi.str).


----- "Luis Agullo (LAB)" <> wrote:

| From: "Luis Agullo (LAB)" <>
| To:
| Sent: Thursday, October 15, 2009 8:49:58 AM GMT -05:00 US/Canada Eastern
| Subject: namd-l: ATP and Stream files
| I have problems with ATP in NAMD simulations. I have read here
| several
| options to solve a similar problem (FATAL ERROR: UNABLE TO FIND ANGLE
| PARAMETERS FOR CN7 CN7B ON6B). Apparently, if I am right, the
| cleanest
| solution is to use stream files with specific information for ATP
| (toppar_all27_na_nad_ppi.str). What I do not now is if I need to call
| to
| this stream file from the config file during simulation with NAMD or
| if it
| is sufficient to use it during psf generation.
| Luis

Dimitar V Pachov
PhD Candidate
Physics & Biochemistry Department     Phone: (781) 736-2326
Brandeis University, MS 057           Email:

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