Re: [AMBER] Is it a bug in the xleap of AmberTools 1.2 and 1.4.

From: case <>
Date: Mon, 21 Jun 2010 09:51:50 -0400

On Mon, Jun 21, 2010, Catein Catherine wrote:
> In the pdb file, I named the terminal DNA bases as DA, with PO2 using
> the atom name of P and O1P and O2P.

You need to look at the library you are loading, as well as the leaprc file
(since the latter probably contains aliases that leap uses to try to
understand what is in pdb files.) If you are using version 1.2, be sure
to download bugfix.12.

However, it sounds like you have phosphates at terminal residues of DNA,
which may not match the usual conventions in the library. Without knowing
more about what is in the pdb file you are trying to load, it is hard to be
of much help. As a (wild?) guess, note that the leaprc file will probably
alias a terminal DA residue to DA5, which doesn't have any phosphate group.
You may need to edit the leaprc file to prevent that from happening --edit
the addPdbResMap section.


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Received on Mon Jun 21 2010 - 07:00:06 PDT
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