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

From: Ross Walker <>
Date: Wed, 11 Mar 2009 13:25:47 -0700

Hi Joe,

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

This looks reasonable to me. It might be useful to include something along
the lines of OPTIONAL INFO in the comment line to imply that this info is
really here just for informational purposes or for completeness and isn't
required for actual simulation.

Note it would be good if ptraj and ambpdb were ultimately updated to read
this info so that they could write back a complete pdb rather than a
truncated one.
> 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.

I agree here and there is no need for it to be exactly the same as the pdb
limit although it might be useful to limit it to the column space that is
assigned to it in the pdb file format.
> One field I left out is the altid, but that should map directly to
> LES_ID, 0->' ', 1->'A', 2->'B', ...

Altid probably shouldn't get propogated to the pdb file. Note we encourage
users to massage the pdb files quite a bit before loading them into leap.
Common practice is to clean up a lot of unnecessary info from the pdb file
including REMARKS, CONNECT info etc BEFORE loading it into leap since leap
doesn't currently process any of this info. Additionally in the case of
alternate ID's we tell the user that they have to pick one themselves and
then edit the pdb to remove all the alternatives and then remove the 'A' or
'B' etc from the front of the residue ID. I haven't checked leap's behaviour
with respect to alternate IDs whether it moans that it doesn't recognize the
residue or it just picks the first altID or it reads both and moans about
creating a lot of duplicate atoms. In reality I think it is better to force
the use to have to make a choice at the pdb level. This stops it being too
'black box'.

All the best

|\oss Walker

| Assistant Research Professor |
| San Diego Supercomputer Center |
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Received on Fri Mar 13 2009 - 01:14:01 PDT
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