Re: [AMBER] Leap question/suggestion for leap developers

From: David A Case <>
Date: Mon, 13 Jun 2011 08:37:40 -0400

On Sun, Jun 12, 2011, Sergio R Aragon wrote:
> Adding residues to a protein whose pdb file shows some to be missing is
> a typical problem encountered by many researchers studying proteins.
> While the package "modeller" seems capable of doing this in the general
> case, many simple cases can be done within leap. These are the cases
> when the peptides to be added are very short.

Thanks for the suggestions. However, what you propose is not a simple
change, and a real implementation would lead to lots of complex problems,
both in terms of algorithm and in terms of documentation. Basically,
LEaP is primarily a program to read in structural models you have already
built. It has a very modest and primitive ability to do a few common
things, like adding hydrogens, or a missing OXT atom at the end of a
chain. Given that there are quite a few homology modeling programs
available, our general advice is to try to use those for the sorts of problems
you describe.

In particular, inserting coordinates into the middle of an existing sequence
involves rather complicated steps to get both ends aligned with what is
already there. This is a classic "loop building" procedure that has many
possible solutions; as you note, none of them are incorporated into LEaP.


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Received on Mon Jun 13 2011 - 06:00:04 PDT
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