Re: [AMBER] loadpdb and SSBOND

From: David A Case <>
Date: Thu, 16 Dec 2021 09:14:33 -0500

On Wed, Dec 15, 2021, Alan wrote:

>I'm wondering how robust is loadpdb (from tleap).
>Does it parse any information from a PDB header? If so, which ones?

tleap does make use of the CONECT records (which are not part of the
header). The general workflow is that pdb4amber will find SS bonds and
create the needed CONECT records.

I don't think that tleap makes any other use of the header info. Scott
Brozell, who follows this list, is our tleap guru.

>If it's about a volunteer to tackle that, well I may try. Or is it already
>under work?

I'll leave this one for Scott; but volunteers are certainly welcome. My
general feeling is that tleap is probably not the right place for such
changes. We should pre-process input PDB files, probably an
expanded/updated version of pdb4amber, to create a "simplified" PDB file
that tleap can handle. The pre-processor would probably be a python script,
and could take advantage of a lot of functionality that is already in

In fact, getting a next-gen version of pdb4amber, that could (as an example)
handle carbohydrates, is near the top of my "Amber to-do list".

>Please, just give me some heads up, like which source file to look at.

You could do 'grep -i ssbond *.c' in
amber20_src/AmberTools/src/leap/src/leap. It looks like tleap recognizes
SSBOND cards, but doesn't do anything with that information. I'm open to
counterarguments, but I don't think tleap is a very easy place to start
making significant changes.

Thanks for the question.


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Received on Thu Dec 16 2021 - 06:30:02 PST
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