AMBER Archive (2006)

Subject: Re: AMBER: internal coordinates

From: David A. Case (case_at_scripps.edu)
Date: Mon May 01 2006 - 15:50:10 CDT

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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