Hi Filip,
Thank you for that explanation. One question for you still, is the
improper for the methyl group missing from the DMC parameters? I've added
it for my work, but it would be nice to add it to the dmc.frcmod file in
the contributed parameters database so others can benefit as well. Thanks.
Sid
Sid
On Mon, Mar 31, 2014 at 1:53 AM, Filip Lankas <filip.lankas.uochb.cas.cz>wrote:
>
> > Just as a note: Richard Bryce maintains the contributed parameters web
> site,
> > but the actual parameters come from many places, as noted in the links
> > provided there. The DMC files come from F. Lankas, T.E. Cheatham III, N.
> > Spackova, P. Hobza, J. Langowski, J. Sponer. Biophys. J. 2002
> 82:2592-2609.
> >
> > ....dac
> One more remark: The DMC parameters in the original paper were intended
> for use with parm94 (look at the date - those were the days ...)
>
> However, my student Tomas Drsata and I have updated the parameters, so
> that the parameter files on the contributed parameter web page are now
> fit for use with parmbsc0.
>
> The update concerns the backbone only and has nothing to do with the
> methylated cytosine base itself, which stays the same as in the original
> paper. We just replaced the parm94 backbone with the parmbsc0 backbone,
> to save the user from doing it themselves.
>
> Filip
>
> --
> ------------------------------------------------------
> Dr. Filip Lankas
> Institute of Organic Chemistry and Biochemistry
> Flemingovo nam. 2
> 166 10 Praha 6
> Czech Republic
>
> Phone: +420 - 220 410 319 Fax: +420 - 220 410 320
> E-mail: filip.lankas.uochb.cas.cz
> Web page:
> www.uochb.cz/web/structure/430.html?do[loadData]=1&itemKey=en_40
>
> Secretary: Helena Cerna, phone +420 - 220 410 321
> helena.cerna.uochb.cas.cz
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Received on Mon Mar 31 2014 - 14:00:04 PDT
