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

From: David A. Case <>
Date: Thu, 12 Mar 2009 07:28:45 -0400

On Wed, Mar 11, 2009, Joe Krahn wrote:

> Here is my suggestion for including PDB data in the PRMTOP file.

Don't forget that we need some sort of "not applicable or not available"
tag for most of these. First, many structures don't have an associated
PDB file. Even if they do, we add many atoms (hydrogens, waters, ions,
etc.) that won't have any associated residue numbers, b-factors,
occupancies, etc. For hydrogens, it probably makes sense to assign
residue numbers, chain ids etc to be the same as the atoms they are
bonded to; less clear what to do with all the waters.

> %COMMENT The element as read from columns 77-80 of the pdb file
> %FORMAT(5E16.8)
  ^^^^^^^^^^^^^^ typo?

> One field I left out is the altid, but that should map directly to
> LES_ID, 0->' ', 1->'A', 2->'B', ...

I don't think we should promote confusion between LES_ID and ALTID. $.02....dac

AMBER-Developers mailing list
Received on Fri Mar 13 2009 - 01:22:25 PDT
Custom Search