For NA, valid citation of the latest parmbsc0 version is
Refinenement of the AMBER force field for nucleic acids: Improving the description of alpha/gamma conformers
Author(s): Perez A, Marchan I, Svozil D, et al.
Source: BIOPHYSICAL JOURNAL Volume: 92 Issue: 11 Pages: 3817-3829 Published: JUN 1 2007
probably together with the Cornell et al 1995 paper.
I am still not 100% sure what is best to give for parm99 NA ff,
as it seems to me that the main effort has been done in Cheatham et al
J. Biomol. Struct. Dyn. 1999
Any advice?
Jiri
[ Charset ISO-8859-1 unsupported, converting... ]
> Hi William,
>
> This info is all in the manual. See:
>
> http://ambermd.org/doc11/AmberTools.pdf
>
> In chapter 2 all of the force fields are discussed along with citations for
> each one. E.g.:
>
> ff99SB is the recent attempt to improve this behavior, and was developed in
> the
> Simmerling group.[15]
>
> Ref 15: Hornak, V.; Abel, R.; Okur, A.; Strockbine, B.; Roitberg, A.;
> Simmerling, C. Comparison
> of multiple Amber force fields and development of improved. Proteins, 2006,
> 65,
> 712?725.
>
> Gaff is similarly there.
>
> [69] Wang, J.; Wolf, R.M.; Caldwell, J.W.; Kollamn, P.A.; Case, D.A.
> Development and
> testing of a general Amber force field. J. Comput. Chem., 2004, 25,
> 1157?1174.
>
> AMBER11:
>
> D.A. Case, T.A. Darden, T.E. Cheatham, III, C.L. Simmerling, J. Wang, R.E.
> Duke, R.
> Luo, R.C. Walker, W. Zhang, K.M. Merz, B. Roberts, B. Wang, S. Hayik, A.
> Roitberg,
> G. Seabra, I. Kolossv?ry, K.F. Wong, F. Paesani, J. Vanicek, J. Liu, X. Wu,
> S.R. Brozell,
> T. Steinbrecher, H. Gohlke, Q. Cai, X. Ye, J. Wang, M.-J. Hsieh, G. Cui,
> D.R. Roe, D.H.
> Mathews, M.G. Seetin, C. Sagui, V. Babin, T. Luchko, S. Gusarov, A.
> Kovalenko, and
> P.A. Kollman (2010), AMBER 11, University of California, San Francisco.
>
> AMBER10:
>
> D.A. Case, T.A. Darden, T.E. Cheatham, III, C.L. Simmerling, J. Wang, R.E.
> Duke, R. Luo,
> M. Crowley, R.C.Walker,W. Zhang, K.M. Merz, B.Wang, S. Hayik, A. Roitberg,
> G. Seabra, I.
> Kolossv?ry, K.F.Wong, F. Paesani, J. Vanicek, X.Wu, S.R. Brozell, T.
> Steinbrecher, H. Gohlke,
> L. Yang, C. Tan, J. Mongan, V. Hornak, G. Cui, D.H. Mathews, M.G. Seetin, C.
> Sagui, V. Babin,
> and P.A. Kollman (2008), AMBER 10, University of California, San Francisco.
>
> All the best
> Ross
>
> > -----Original Message-----
> > From: William Flak [mailto:williamflak.yahoo.com]
> > Sent: Sunday, October 03, 2010 4:16 PM
> > To: AMBER
> > Subject: [AMBER] Citations
> >
> > Dear AMBER
> > It may be a naive question, but I see most of the authors don't write a
> > citation for amber force field. And I couldn't find some specific
> citations
> > (ff99SB).
> > If you don't mind, could you help me and tell me where I can download the
> > complete citations of:
> > AMBER force field 99SB
> > Gaff force field
> > and
> > AMBER 10 software?
> > Thanks in advance
> > W. Flak
> >
> >
> >
> >
> >
> >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
>
>
> _______________________________________________
> AMBER mailing list
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> http://lists.ambermd.org/mailman/listinfo/amber
>
>
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Received on Mon Oct 04 2010 - 02:30:05 PDT
