From: Dimitar V Pachov (dpachov_at_brandeis.edu)
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).
Dimitar
----- "Luis Agullo (LAB)" <lab_at_lagullo.com> wrote:
| From: "Luis Agullo (LAB)" <lab_at_lagullo.com>
| To: namd-l_at_ks.uiuc.edu
| 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: dpachov_at_brandeis.edu ========================================================
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