AMBER Archive (2006)

Subject: RE: AMBER: A dummy atom on the center of solute molecule

From: Ilyas Yildirim (yildirim_at_pas.rochester.edu)
Date: Tue May 30 2006 - 18:06:54 CDT

Dear Acci,

> Then I prepared prep file and frcmod file which contains DH(dummy atom). I
> can understand that I have to change bond parameter in frcmod file as
> following,
>
> -------frcmod file---------
> remark goes here
> MASS
> DU 0.000 0.000 ATTN, need revision
>
> BOND
> c2-DU 0.00 0.000 ATTN, need revision
>
> ANGLE
> c3-c2-DU 0.000 0.000 ATTN, need revision
> c2-DU-c2 0.000 0.000 ATTN, need revision
> c2-c2-DU 0.000 0.000 ATTN, need revision
> ha-c2-DU 0.000 0.000 ATTN, need revision
>

These have zero parameters. I dont think that these are useful parametes.

What kind of a dummy atom is this? Hydrogen type, Carbon type, etc? After
deciding on that, what do u want to do with this dummy atom? Creating a
dummy atom is very easy, but before going to creating a dummy atom part, u
have to know for what this dummy atom is going to be used.

I checked out your files, and there is a residue, BUT in it. First create
a BUT.lib file; then manipulate that residue by including a dummy atom and
create a new BUT_new.lib file. While adding a dummy atom, be sure that u
connect that dummy atom to the atoms u are interested. 

-- 
  Ilyas Yildirim
  ---------------------------------------------------------------
  - Department of Chemisty       -				-
  - University of Rochester      -				-
  - Hutchison Hall, # B10        -				-
  - Rochester, NY 14627-0216     - Ph.:(585) 275 67 66 (Office)	-
  - http://www.pas.rochester.edu/~yildirim/			-
  ---------------------------------------------------------------

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