Re: regenerating PSF file

From: Cetin Baloglu (baloglu_at_gmail.com)
Date: Wed May 18 2005 - 02:50:38 CDT

Thanks for the answer Michael,
Actually I am curious about non-covalent bonds. Do psf files contain
information about these bonds and the related atoms? Also angles,
dihedral angles changes but with the same psf file we use the same
values. I saw discover in insightII producing the protein structure
file after md is done and this made me think about regenerating the
psf file.

On 5/18/05, Michael Grabe <mgrabe_at_itsa.ucsf.edu> wrote:
> Cetin,
>
> do you break these bonds by hand? if so, then you certainly
> need to generate new psf files, but no bonds will be breaking
> during your high temperature runs.
>
> -michael
>
> On May 17, 2005, at 11:07 PM, Cetin Baloglu wrote:
>
> > Hi,
> >
> > I am doing simulations to observe temperature effects on proteins. I
> > use same psf file for every experiment, which inputs are outputs of
> > previous experiments. However, I am thinking if this is a mistake or
> > not as psf file contains bond information that is to be broken in high
> > temperatures.
> >
> > Cetin Baloglu
> >
> >
> >
> ------------------------------------------------------------------------
> --------------------------
> Michael Grabe, Ph.D.
> Post-doctoral Fellow
> Howard Hughes Medical Institute
> University of California, San Francisco
> 1550 4th Street GD482
> San Francisco, CA 94143
> mgrabe_at_itsa.ucsf.edu
> tel: ++ 415.476.4021
> http://itsa.ucsf.edu/~mgrabe
>
>

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