Re: ATP and Stream files

From: L. Michel Espinoza-Fonseca (mef_at_ddt.biochem.umn.edu)
Date: Fri Oct 16 2009 - 00:42:52 CDT

Luis,

Before using the stream files please take a look at the "readme" file before
using them. There it clearly says that you need to use in combination with
protein force field via the top_all27_prot_na.rtf (for psf generation) and
par_all27_prot_na.rtf (for actual simulation). Most likely the error is
caused by not including par_all27_prot_na.rtf in your input file.

Cheers,
Michel

On Thu, Oct 15, 2009 at 2:49 PM, Luis Agullo (LAB) <lab_at_lagullo.com> wrote:

> 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
>
>

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