Re: [AMBER-Developers] Including chain and residue numbers in the PRMTOP

From: David A. Case <>
Date: Fri, 6 Mar 2009 09:46:01 -0500

On Thu, Mar 05, 2009, Joe Krahn wrote:

> I think it would be useful to include the ChainID and residue number in
> the PRMTOP. It makes selections much easier for defining restraints, and
> would enable writing a complete PDB file directly from the PRMTOP file.
> At least some other AMBER users think it is a good idea. Is there any
> reason not to include the extra atom/residue data?

The reason with tleap was that the code was inpentrable -- it was not
simply a matter of adding some more fields to an "atom" struct
someplace. Data was passed around from one container to another and it
was beyond my abilities to figure out how to save such information.

I assume that Wei can more readily add such info to sleap, since he
knows the data structures that are used. But it's still tricky to know
how to handle such information. When does one use internal residue
numbers (starting at 1) and when to use those in the pdb file. Should
they be named different things? What to do when residue numbers are not
"numbers" at all? What does that do to the concept of ranges of
residues (used in mask commands, etc.) It's something that will require
a bit of fiddling to get right. Don't forget that anything that is done
has to be very clearly explained in the Users' Manual.


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Received on Sun Mar 08 2009 - 01:08:45 PST
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