Re: [AMBER] changeLJSingleType problem in parmed.py

From: Jason Swails <jason.swails.gmail.com>
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: http://jswails.wikidot.com/parmed#toc4

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.

HTH,
Jason

-- 
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Thu Dec 12 2013 - 15:00:02 PST
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