Here is my suggestion for including PDB data in the PRMTOP file. Some of
these are not useful to general users, so I think it is OK to skip some
of these in the standard Leap tools.
Residue properties:
%FLAG RESIDUE_CHAINID
%COMMENT The ChainID as read from the pdb file
%FORMAT (20A4)
...
%FLAG RESIDUE_NUMBER
%COMMENT The residue number as read from the pdb file
%FORMAT (10I8)
...
%FLAG RESIDUE_INSCODE
%COMMENT The residue number insertion code as read from the pdb file
%FORMAT (20A4)
...
Atom properties:
%FLAG ATOM_BFACTOR
%COMMENT The atom B-factor as read from the pdb file
%FORMAT(5E16.8)
...
%FLAG ATOM_ANISOU
%COMMENT The atom anisotropic temperature-factor from the pdb
%COMMENT AINSOU record. There are 6 values per atom.
%FORMAT(5E16.8)
...
%FLAG ATOM_OCCUPANCY
%COMMENT The atom occupancy as read from the pdb file
%FORMAT(5E16.8)
...
%FLAG ATOM_ELEMENT
%COMMENT The element as read from columns 77-80 of the pdb file
%FORMAT(5E16.8)
...
I left chainid and inscode as 4-character strings to keep compatible
with the existing string tokens, and because 1 character is often not
sufficient. Other file coordinate file formats already allow for more
than 1 character.
One field I left out is the altid, but that should map directly to
LES_ID, 0->' ', 1->'A', 2->'B', ...
Joe
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Received on Fri Mar 13 2009 - 01:13:49 PDT
