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

From: Ilyas Yildirim <>
Date: Tue, 23 May 2006 22:49:00 -0400 (EDT)

Dear Acci,

Placing a dummy atom is very easy, in fact. I would suggest you to do the
following: (I guess u mean by ligand either RNA or DNA) In your .pdb
file, put a TER card to seperate the ligand and protein. This way,
leap will understand that there are 2 seperate molecules in the .pdb
file. Write a small leap script like the following:
------------- -------------------
source leaprc.ff99
molecule = loadpdb <name of the .pdb file>
In the terminal window, run xleap as follows;

$ xleap -f

This will load the ff99 force field (so, choose the right force field for
your case). If your .pdb file's atom naming is same as LEAP's atom
naming, it should not give any important messages (it will probably try
to put H atoms, which is normal). If there are some other messages like
if leap is trying to put some heavy atoms, you have to check out your
.pdb file, and see where the problem is. Assuming that there arent any
error messages in xleap, type 'edit molecule' in xleap window. This will
pop up a new window, which will show your ligand and protein.

Rotate your structure and zoom into the place where you want to put the
dummy atom. Click on the 'draw' button and choose any atom (say H), and
click on the place where you want to put this atom. Then click on the
'select' button and select the placed atom. Goto Edit>Edit Selected Atoms.
This will popup a new window, which will show you the properties of the
selected atoms. Now, you can change the name,type,charge,etc. of this
atom. Name it something like DH, and for the type, write 'DH' (or any
atom type name u wanna create). For the element part, write '?'. This will
mean that this atom is not a known element. Then goto Table>Save and Quit.
Close the edit window. In the xleap window, write 'savepdb molecule
molecule_new.pdb' which will save it to a .pdb file. If you check out the
molecule_new.pdb file in the terminal window, u will see the new atom DH
included in the file.

In my previous email, I asked exactly what u wanted to do with the dummy
atom. Is it going to be part of the ligand, or something like a Na+ atom?
If you dont connect this dummy atom to the ligand or protein, during the
MD simulation, it will move away from the place where u put the atom. So,
if you want to keep this dummy atom in a particular region/position, you
have to connect it to the neighbouring atoms. Moreover, u have to specify
the missing parameters of this dummy atom, such as the charge of the dummy
atom, bond length parameters, angle parameters, dihedral and torsional
parameters, etc. Without giving these missing parameters, xleap wont be
able to understand the dummy atom. That said, you have to create a
modified force field file, aka .frcmod file. Check out the following web
address to learn more about frcmod file:

Hope this might answer some of your questions. Good luck.

On Wed, 24 May 2006, Atsutoshi Okabe wrote:

> Dear Ilyas,
> Thank you for your quick response.
> I want to simulate keeping the particular distance between the mass center
> of solute(ligand) and protein. So, I need to put the dummy atom on the
> center of ligand molecule. But I don't know how I should set a dummy atom in
> pdb file and how I should make a prep file.
> Could you please give me any suggestion?
> Acci Okabe
> -----Original Message-----
> From: [] On Behalf Of
> Ilyas Yildirim
> Sent: Monday, May 22, 2006 8:58 PM
> To:
> Subject: Re: AMBER: A dummy atom on the center of solute molecule
> Can you explain a little bit more on the structure and the dummy atom? Is
> it going to be part of the solute, or is it going to have some distance
> restraints to keep it in a particular region of the solute?
> On Mon, 22 May 2006, Atsutoshi Okabe wrote:
> > Dear all.
> >
> >
> >
> > Hi.
> >
> > I want to do umbrella sampling MD along the reaction coordinate between
> > protein and
> >
> > the center of ligand molecule.
> >
> > So I need to set a dummy atom on the center of ligand molecule.
> >
> > How should I put a dummy atom in pdb file in Amber8?
> >
> >
> >
> > Could you please give me any suggestions?
> >
> > Thank you.
> >
> >
> >
> > Acci Okabe
> >
> >
> >
> >

  Ilyas Yildirim
  - Department of Chemisty       -				-
  - University of Rochester      -				-
  - Hutchison Hall, # B10        -				-
  - Rochester, NY 14627-0216     - Ph.:(585) 275 67 66 (Office)	-
  -			-
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Received on Wed May 24 2006 - 06:07:17 PDT
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