AMBER Archive (2006)

Subject: Re: AMBER: internal coordinates

From: Ioana Cozmuta (icozmuta_at_mail.arc.nasa.gov)
Date: Tue May 02 2006 - 13:01:45 CDT

Hi,

Thank you very much for the info! From a quick look in the paper referenced below it seems as if the coordinates in nucgen.dat correspond to some rescaled cylindrical coordinates, R, phi, Z.
The only value that is (almost) the same in nucgen.dat and in the paper is that of R. For phi and Z it is not straightforward what has happened.
I'll check the other softwares, it might indeed be much more worthwhile.

Thank you,
Ioana

******
The basic reference source for the fiber-diffraction input is here:

Arnott, S.; Campbell Smith, P.J.; Chandraseharan, R. in Handbook of
Biochemistry and Molecular Biology, 3rd Edition. Nucleic Acids--Volume
II, Fasman, G.P., ed. (Cleveland: CRC Press, 1976), pp. 411-422.

As I remember, the "nucgen.dat" data was copied directly from these tables,
so that might help you decode them.

...good luck...dac

David A. Case wrote:
> Date: Sun, 30 Apr 2006 11:18:19 -0600 (Mountain Standard Time)
> From: Thomas Cheatham <tec3_at_utah.edu>
> To: amber_at_scripps.edu
> Subject: Re: AMBER: internal coordinates
>
>
>> Does anybody happen to know what each of the columns in the
>> $AMBERHOME/dat/leap/parm/nucgen.dat
>>
>
> I have no idea and note that looking at the source code for nucgen.f (which is
> usually a very good / critical place to look beyond the manuals) doesn't help
> much. This code was written back in 1985 and hasn't really changed much since
> then... You could experiment, but my recommendation is to use another program
> to build the helices.
>
>
> 3DNA - http://rutchem.rutgers.edu/~xiangjun/3DNA/
>
> A nice program by Xiang-Jun Lu that not only can analyze
> nucleic acid structure well, but generate models with
> fiber or user supplied parameters for arbitrary twist or
> alteration of helicoidals...
>
> NAB - nucleic acid builder "language" by Dave Case's group,
> the link at http://www.scripps.edu/mb/case/ under NAB.
>
> This is not a program per se, but a language that allows
> you to build arbitrary nucleic acid structures. Although
> there is a learning curve, the language includes the
> concepts of energy / minimization (i.e. it includes a full
> generalized Born implicit solvent model including second
> derivatives!!!) and interfaces to AMBER.
>
>
> Learning either one (or both) of these will be significantly more general and
> useful than trying to reverse engineer nucgen...
>
>
> \-/ Thomas E. Cheatham, III (Assistant Professor) College of Pharmacy
> -/- Departments of Med. Chem. and of Pharmaceutics and Pharm. Chem.
> /-\ Adjunct Asst Prof of Bioeng.; Center for High Performance Computing
> \-/ University of Utah, 30 S 2000 E, SH 201, Salt Lake City, UT 84112
> -/-
> /-\ tec3_at_utah.edu (801) 587-9652; FAX: (801) 585-9119
> \-/ BPRP295A http://www.chpc.utah.edu/~cheatham
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-- 
Ioana Cozmuta, Ph.D
Eloret Corporation
NASA Ames Research Center
Mail Stop 230-3
Moffett Field, CA  94035
phone (650) 604-0993
e-mail: icozmuta_at_mail.arc.nasa.gov
http://people.nas.nasa.gov/~ioana/

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