Dave - I think my modification and how the modification is done should be
included in the User's Manual. At the end, people trying to use the force
field will directly use ff10. Without my revision, people who created the
chi-OL revision would not be aware of the importance of the chi torsion,
and, therefore, my modification should be included in the manual.
I can provide you the necessary files (.lib, frcmod, etc.) so that anyone
who wants to use my modification can easily access it. Please let me know
whom and which files to send. I can also provide test cases if it is
needed.
Sincerely,
Ilyas Yildirim, Ph.D.
-----------------------------------------------------------
= Department of Chemistry - 2145 Sheridan Road =
= Northwestern University - Evanston, IL 60208 =
= Ryan Hall #4035 (Nano Building) - Ph.: (847)467-4986 =
=
http://www.pas.rochester.edu/~yildirim/ =
-----------------------------------------------------------
On Mon, 28 Mar 2011, David A Case wrote:
> On Sun, Mar 27, 2011, yildirim.pas.rochester.edu wrote:
>>
>> Even though I am the first to publish and show the importance
>> of the chi revision, ff10 with the references Jason gave imply that they
>> found out the problem on chi torsion.
>
> I don't think the implication you state is correct. The references in the
> Users' Manual point people to the papers that are most directly relevant to
> the force fields we support. There is no way that the Users' Manual should be
> considered as a review of the field, or that failure to cite some paper
> implies anything about its general contribution to the field.
>
> That said, we certainly want the Users' Manual to help Amber users find
> important information, and I have asked the ff developers (who follow this
> mailing list) to review how ff10 is described there, in anticipation of
> the release of AmberTools 1.5 in a few weeks. For proteins, we provide
> LEaP input files and instructions for several torsion modifications
> (which were provided by their developers), and the same could be done for
> alternate RNA chi parameterizations.
>
> ...best regards...dac
>
>
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Received on Mon Mar 28 2011 - 11:30:02 PDT
