AMBER Archive (2006)

Subject: Re: AMBER: xleap

From: David A. Case (
Date: Tue Nov 28 2006 - 10:02:13 CST

On Tue, Nov 28, 2006, Steve Seibold wrote:
> Is there a way to change HIE to HID "in" xleap? That is without going
> "edit unit". I have looked at "help" in xleap, but cannot determine if I
> can do this or not.
> I realize I could just change the pdb file, but I already have whole
> molecule (very large!) with metals etc coordinated to residues etc in
> xleap and was hoping not to have to scratch all the work to go back to
> pdb file.

If you want to change *all* HIE to HID, you could use the addPdbResMap
command, something like

addPdbResMap {
    { "HIE" "HID" }

But there is no easy way to just change certain histidines (e.g. those bonded
to metals) and leave others alone.

I don't know what you mean by "scratch all the work to go back to the pdb
file". If you didn't save your leap commands in a file for re-use later, this
will be a good learning experience :-). You can generally go through the
leap.log file and extract the commands used by the previous run; try this

     grep '^>>' leap.log >

Then edit the file to be sure it does what you want. Then you can
take rerun all the things you did before on your modified pdb file.


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