AMBER Archive (2006)

Subject: Re: AMBER: how to mutate in amber 8 for thermodynamic integration without using xleap

From: David A. Case (case_at_scripps.edu)
Date: Wed Jul 26 2006 - 12:44:58 CDT

On Tue, Jul 25, 2006, Lwin, ThuZar wrote:
>
> I am learning how to do thermodynamic integration using amber8. I would
> like to mutate Alanine to Glycine by mutating the side chain CH3 to H.
> Here is what I did in tleap. Please let me know what I am doing wrong.
>
> a = sequence{ALA}
> set a.CB pertName HA3

The syntax is unit-name.residue.atom-name, e.g. "a.1.CB", not "a.CB".

However, I really recommend that you use xleap, visually select all atoms
in your structure, and use the "edit selected atoms" command. That will
give you a spreadsheet that shows which things need to be modified.

And, if you are thinking long-range, it would be good to update to Amber 9,
since the way in which thermodynamic integration is implemented is quite
different there.

...regards...dac

-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu