AMBER Archive (2006)

Subject: Re: AMBER: prepin format

From: David A. Case (case_at_scripps.edu)
Date: Fri Mar 10 2006 - 00:49:22 CST

On Thu, Mar 09, 2006, nkyx_at_sohu.com wrote:

> A question I'd like to know is whether the Cartesian coordinate can
> be used in prepin file.

In principle, yes. The file format descriptions can be found on the Amber
web site (look for the "file formats" link). See the variable INTX with
controls whether internal or Cartesian coordinates are used.

The caveat is that, as you note, this option is almost never used, so there
may be bugs.

[Further, we are encouraging folks to use the mol2 format, rather than the prep
format, if at all possible. The prep format may well be retired as soon as
Amber 10. The mol2 format is widely used, and is much easier to understand.
The main drawback right now is limited support in Amber for mol2 files that
have lots of molecules or residues in a single file.]

...good luck...dac

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