Re: AMBER: amber file formats.

From: David A. Case <>
Date: Thu, 20 Oct 2005 09:20:36 -0700

On Thu, Oct 20, 2005, Shishir wrote:

> My problem is this: I have a (.top+.crd) file which I want to load in
> xleap to make a few changes to topology of the system. Can it be done
> some other way? (since xleap doesn't loads a .top/.crd file)

Topology (prmtop) files contain detailed information about potentially complex
molecular systems. As you note, LEaP was not designed to use these as inputs.
The expectation is that you would save the files you used to create the prmtop
file in the first place, and use those to re-create a modified prmtop file
when necessary.

In this sense, a prmtop file is something like a pdf file for documents: the
pdf file describes to a printer how to print the page, but it is not indented
that modifications be made by editing the pdf file. Rather, you change the
document by creating a new pdf file from some other program (such as a
word-processing program.)

> I didnot know the solution for this so i cut off some code from ptraj and
> wrote a (.top/.crd) to .lib converter (for ptraj reads .top/.crd files and
> has dumping function for many fields)

It is certainly true that (in spite of what I argued above) that it would at
times be very useful to be able to modify prmtop files without having the
original files around. Your code might be useful to others in this regard.
But it is hard to get completely correct: prmtop files store completely
different information than do .lib files: the latter are designed to store
information about units (molecules or residues) that will be combined to make
a molecular system. The former has the details about the combined system, but
not necessarily all the information that the original .lib files had.

[To continue my analogy: there *are* programs that parse pdf files and extract
text or images from them. But these are only partially successful, since much
of the logical information about text layout that was present in the
word-processor that created the pdf file is no longer present in the pdf
output. The same holds for prmtop files.]

> Then there is the question of overall usage. Why cannot we have a single
> file format throughout all of the amber? like .crd/.top files.

See above. Topology files contain different sorts of information than do mol2
or .lib files.


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Received on Thu Oct 20 2005 - 17:53:01 PDT
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