AMBER Archive (2005)

Subject: Re: AMBER: amber file formats.

From: Shishir (shishirk_at_gmail.com)
Date: Thu Oct 20 2005 - 15:37:16 CDT

Dear David,
   Thanks for your reply. Here are some more questions:

- what is the unit of force in Amber (say as it is stored in force arrays
used in code)? is it pN? if we take Kcal/mole, Angs to be our units
then 1Kcal/mole/Angs ~ 69.5 pN / species? (there may be a conversion
factor for reduced units).

- what is the ordering of connectivity and hierarchy fields in .lib files.
(I guess this doesn't matter and this order should most probably be
inherited from the .pdb spec. but it doesnot match).

and .lib files seem to have a subset of information from .top/.crd and
not different one - if you know every detail on how to build a system
(a .top file) then you have information about the components the system
uses (a .lib file). .lib is probably used only because it's simpler, smaller,
legacy - all three of these can be argued against. (btw, I am not
convinced of your analogy here, pdf was never designed to be
modifiable - it preserves author's intentions, machine dependent
things. I would like .top to be compared to tex files. further if pdf is
lossless then Adobe must be having programs to decode pdfs and
people have use for it).

- about the documentation of the code itself. is there something like this
open to public? (there must be something for developers, as such a code
is hard to modify without documentation). at least a dictionary of variable
names and their intended usage will be very helpful.

thankyou very much,
Shishir.

On 10/20/05, David A. Case <case_at_scripps.edu> wrote:
> 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.
>
> ...dac
>
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