RE: AMBER: Free energy for part of the system

From: jialei <>
Date: Tue, 4 Dec 2007 18:21:03 +0000

Thank you very much Dave. We would like to compare free energies between two duplexes (one target duplex and one control). The reason why we thought out computing the central 5mer free energy is that there are end effects during the simulation, while the central 5mer looks normal. So we would like to computer the "free energy" represents the certral 5mer part and compare it with that of the control.
I understand there will be two pairs of broken covalent bonds if I just cut the central 5mer out. And I could not cap the ends with hydrogens since the simulation trajactory does not have them. Is it still valid if I just make a comparison between "free energies" of the parts as I will define them? Should the broken covalent bond affects the intrinsic MM-PBSA calculation and further affects the comparison? Thank you again.
Lei Jia> Date: Mon, 3 Dec 2007 18:35:50 -0800> From:> To:> Subject: Re: AMBER: Free energy for part of the system> > On Mon, Dec 03, 2007, jialei wrote:> > > > We are simulating an 11mer DNA duplex with AMBER9 and willing to compute the> > free energy of the DNA central 5mer by MM-PBSA. I am aware that the MM-PBSA> > has a ligand and receptor selection function to compute the binding energy.> > However, the DNA central 5mer is covalently linked to the rest of DNA. So> > the MM-PBSA does not simply work for this problem. Is there an easy way to> > computer the part DNA's free energy? Thank you very much for the help!> > > > The only relevant quantities that can be computed are free energy> *differences*, and it is not clear what the two end points you are considering> are.> > You will need to think carefully about how you want to define the free energy> of part of a molecule, and what you would do with such a number once you> estimated it. I!
 t might be possible to make a useful definition (under some> assumptions), but I am pretty sure that there is no "easy way" to do this.> > ...dac> -----------------------------------------------------------------------> The AMBER Mail Reflector> To post, send mail to> To unsubscribe, send "unsubscribe amber" to
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Received on Wed Dec 05 2007 - 06:07:29 PST
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