Re: AMBER: Thermodynamic integration using the amber 9

From: Ilyas Yildirim <>
Date: Mon, 29 May 2006 10:25:21 -0400 (EDT)

Dear Vitor,

In AMBER 9, there is no need to use saveamberparmpert if u want to do TI
calculation. In AMBER 8, it was necessary to create the prmtop file using
saveamberparmpert, but in AMBER 9, u need to create 2 prmtop files: One
for the initial and one for the final states. As a result, u dont need to
use saveamberparmpert, which stores the perturbation information.

> to nothingˇ±. However I would like to do this
> transformation in a single step in which the charges and
> the vdw parameters are changed simultaneously. So, the
> question is it possible to do this with amber 9 using a
> single prompt file (with information about vdw and charge
> variations) created via saveamberparmpert command in
> xleap. If the, the answer is yes, which klambda is the
> most suitable one, 7 ?...

I think this is possible, if u will get a smooth transformation at the
end. For the best klambda values, the best thing to do is to do the
simulation for a couple of klambda values, so that you can see which one
is giving the best (smooth) transformation/path.

> Alternatively, we have to create prmtop files
> corresponding to initial (substrate) and end (nothing,
> with all atoms replaced by dummies) stages and to use the
> ˇ°multistage protocolˇ± as suggested in amber9 manual.
> However, for me it is not no clear how to do to create the
> prmtop files. In other words to use saveamberparm instead
> of saveamberparmpert, is it necessary include the charge
> variations. The lib files corresponding to the
> transformation ethane to methane reported with software
> package amber9/test/ti_eth2meth_gas would be a useful
> contribute for a complete understanding of this issue.

What u need to do is the following: You have 2 states; initial and final
states. For the initial state (let's call it 1.pdb), u need to create the
prmtop file using saveamberparm. For the final state (let's call it
2.pdb), u need to create another prmtop file using saveamberparm. The
important thing is to be sure that the 2.pdb file has the right order. By
that I mean the following: If (let's say) the 84th atom of 1.pdb is H and
has to be perturbed to a dummy atom DH, then, the 2.pdb's 84th atom has
to be DH. Namely, the order of 1.pdb and 2.pdb has to be right.

After creating the prmtop files, u will create a groups file and run your
simulations (see the test cases' c-shell scrips). Hope this helps. Good


  Ilyas Yildirim
  - Department of Chemisty       -				-
  - University of Rochester      -				-
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Received on Wed May 31 2006 - 00:11:57 PDT
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