Re: [AMBER] changeLJSingleType problem in

From: Jason Swails <>
Date: Thu, 12 Dec 2013 17:45:30 -0500

On Thu, 2013-12-12 at 14:26 -0800, Hamed S. Hayatshahi wrote:
> Hi
> It seems that the command changeLJSingleType which is supposed to change the LJ parameters of a selected mask, changes all atoms with the same name/type. For example, in my case, when changing the parameters of :58.Mg+ to x and y as follows, it changes all .Mg+ instead of :58.Mg+ :
> changeLJSingleType :58.Mg+ x y

Yes, this is expected (and documented, to an extent) behavior. ParmEd
van der Waals actions always act on van der Waals types rather than only
those atoms selected in a mask, with the sole exception of "addLJType".

What you seem to want is "addLJType" rather than "changeLJSingleType":

addLJType :58.Mg+ x y

will change _just_ residue 58 Mg to the new Rmin/2, epsilon values. My
wiki has a fairly extensive section regarding van der Waals adjustments
in ParmEd:

I would definitely suggest using some of the introspective commands
(like printDetails, printLJTypes, etc.) to make sure that you are really
making the changes you want to make.


Jason M. Swails
Rutgers University
Postdoctoral Researcher
AMBER mailing list
Received on Thu Dec 12 2013 - 15:00:02 PST
Custom Search