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

From: Joe Krahn <>
Date: Wed, 11 Mar 2009 15:58:18 -0400

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:

%COMMENT The ChainID as read from the pdb file
%FORMAT (20A4)

%COMMENT The residue number as read from the pdb file
%FORMAT (10I8)

%COMMENT The residue number insertion code as read from the pdb file
%FORMAT (20A4)

Atom properties:

%COMMENT The atom B-factor as read from the pdb file

%COMMENT The atom anisotropic temperature-factor from the pdb
%COMMENT AINSOU record. There are 6 values per atom.

%COMMENT The atom occupancy as read from the pdb file

%COMMENT The element as read from columns 77-80 of the pdb file

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', ...


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Received on Fri Mar 13 2009 - 01:13:49 PDT
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