Re: AMBER: Thermodynamic integration using the amber 9

From: Ilyas Yildirim <>
Date: Fri, 2 Jun 2006 16:12:18 -0400 (EDT)

I wrote this response awhile ago, but got an email from The AMBER Mail
Reflector saying that it bounced back. Here is back my response to Vitor's


On Fri, Jun 02, 2006, wrote:

> Date: Mon, 29 May 2006 10:25:21 -0400 (EDT)
> From: Ilyas Yildirim <>
> To: <>
> Subject: Re: AMBER: Thermodynamic integration using the amber 9
> 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
> luck.
> Best,
> Ilyas
> --

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Received on Sun Jun 04 2006 - 06:07:17 PDT
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