From: Chris Harrison (charris5_at_gmail.com)
Date: Wed Jan 19 2011 - 21:24:43 CST
No. It is a problem in either your topology, parameter, or initial
structure file, and subsequently your psf file. Another possiblity is
that you haven't specified the proper parameter file in your config file.
However, your error suggests you have a dihedral in guanine connecting
N1, C2', C2', H2''. Where one C2' is for oxyribose and the other is for
deoxyribose. Check that your input structure is clean and your patch to
convert RNA oxyribose to DNA's deoxyribose has been correctly applied.
-- Chris Harrison, Ph.D. Theoretical and Computational Biophysics Group NIH Resource for Macromolecular Modeling and Bioinformatics Beckman Institute for Advanced Science and Technology University of Illinois, 405 N. Mathews Ave., Urbana, IL 61801 char_at_ks.uiuc.edu Voice: 217-244-1733 http://www.ks.uiuc.edu/~char Fax: 217-244-6078 "S.Archana" <ssarchana_at_imsc.res.in> writes: > Date: Mon, 17 Jan 2011 16:11:27 +0530 > From: "S.Archana" <ssarchana_at_imsc.res.in> > To: namd-l_at_ks.uiuc.edu > Subject: namd-l: Protein-DNA simulations > User-Agent: Internet Messaging Program (IMP) H3 (4.1.3) > > Dear group, > > I have protein-DNA complex to simulate. While minimization, I am > getting an error like this: > > FATAL ERROR: CAN'T FIND DIHEDRAL PARAMETERS FOR HN8 CN8 CN7B NN2G > > There is no such dihedral in the structure. > > topology file used: par_all27_prot_na.prm > > Is this any patch problem while generating the PSF file? > > -- > Thanks & Regards, > Archana > =============================================================== > The real art of conversation is not only to say the right thing > at the right place, but to leave unsaid the wrong thing at the > tempting moment. > =============================================================== > > ---------------------------------------------------------------- > This message was sent using IMP, the Internet Messaging Program. >
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