Re: AMBER: Essential ions and water molecules in MMPBSA computations

From: Cenk Andac <>
Date: Mon, 19 Mar 2007 06:30:00 -0700 (PDT)

Hi Jiri,

Well, thank you for the references you sent. I have read them and I would like to adopt the water inclusion technique discussed in JOURNAL OF THE AMERICAN CHEMICAL SOCIETY 125 (7): 1759-1769 FEB 19 2003 in my MM-PBSA computations.

Before I bombard my further questions, I would like to give a small spiel on what my current system is like: I have a 12-dimer DNA system in complex with a potential anticancer drug, whose X-Ray structure and ITC thermodynamics results have been published.
I have run two sperate 2ns explicite water MD exps for the complex and for its dna (without the ligand) in 0.15 M explicite Na+ environment, provided that excessive positve charges in the system were neutralized by addition of Cl- ions.
According to water(outer)shell computations of ptraj on the dna and the complex, 15 explicit water molecules and 1 Na+ ion are replaced upon binding of the drug.
Also MD for the complex indicates that several water molecules get stuck in the binding site serving as indirect H-bond bridges between the receptor and the ligand.
My MM-PBSA computations between 1500ps and 2000ps, with water molecules and ions removed, resulted in fairly good compensation for DeltaG binding energy, in agreement with the ITC result. However, the MM-PBSA computations seem to fail with the magnitudes of enthalpy and entropy terms of the binding process. And I have this strong feeling that some water molecules and perhaphs 1 Na+ should be explicitely included in the MM-PBSA binding computations.

Here are my questions:
Based on the JACS paper, how did you actually incorporate energy contributions of explicit water molecules in the classical binding free energy equation adopted by MM-PBSA computations shown in EQ.1

receptor + ligand <--> complex
DeltaG=Gcomp - [ Grec + Glig ] EQ.1

I can now think of two plausible ways now, the first way is to make those essential water molecules parts of the receptor, in which case EQ.1 applies in the energy computations, or one could also treat those water molecules as seperate entities and possibly improvise EQ.1 as follows (EQ.2)

DeltaG=Gcomp - [ Grec + Glig + Gwatermolecules,ions,etc. ]

Of course, in the case of EQ.2, computation of Gwatermolecules is another research issue, because the explicitely bound water molecules could be well seperated from each other in implicite environment. In that case, one would have to devise a more practical way to include an average of enthalphy and entropy contributions by one molecule only and perhaphs multiply the average values by the number of replaced (or bound, depending on which method makes more sense) water molecules and include the sum in EQ.2.

I was also wondering what EQ did you actually apply in your MM-PBSA computations. Is there any way that I can perhaps make EQ.2 work on my system? How doable is EQ.2 and what limitations would the latter method have?
Has there been any average absolute Hwater and absolute Swater energy values computed by AMBER before?

I would appreciate your further comments.

My best regards,


Jiri Sponer <> wrote: Waters were included for DNA ligand binding in this work,

Molecular dynamics simulations and thermodynamics analysis of DNA-drug complexes. Minor groove binding between 4 ',6-diamidino-2-phenylindole and DNA duplexes in solution
Author(s): Spackova N, Cheatham TE, Ryjacek F, Lankas F, van Meervelt L, Hobza P, Sponer J
Source: JOURNAL OF THE AMERICAN CHEMICAL SOCIETY 125 (7): 1759-1769 FEB 19 2003

and it seemed to improve results, though the numbers are delicate.
Tom Cheatham will likely comment on it.

Myself, with the waters, I am not fully sure, there are open
issues and likely no perfect solutions. It likely will depend
on the exact nature of your hydration site. Short residency,
long residency, permanent, bridge, pocket, static, dynamical, rattling...

Just few systems with "essential" hydration sites and each hydration event
is absolutely different.
Trapped water molecules are essential to structural dynamics and function of a ribozyme
Rhodes MM et al.
  - internally hydrated cavity.

RNA kink-turns as molecular elbows: Hydration, cation binding, and large-scale dynamics
Razga F et al
Source: STRUCTURE 14 (5): 825-835 MAY 2006
       anharmonic molecular elbow mediated by dynamical water

Long-residency hydration, cation binding, and dynamics of loop E/helix IV rRNA-L25 protein complex
Author(s): Reblova K et al.
Source: BIOPHYSICAL JOURNAL 87 (5): 3397-3412 NOV 2004
             static close to permanent water bridges.

   If you have static water molecule bridging something I would
   probably try to formally include it as a "ligand" and compare
   the results with and without including this water, (using
   trajectory of the "complex").
   See what happens. A salient structural picture is not
   necessarily reflected by large free energy stabilization.

Best wishes, Jiri

[ Charset ISO-8859-1 unsupported, converting... ]
> I got the BIOPHYSICAL JOURNAL 85 (3): 1787-1804 SEP 2003 and it seems to answer my question related to the presence of an essential Na+ ion in complex with a receptor. Thank you.
> My next question was about the presence of an essential water molecule in the binding site. How would one go about inclusion of a very critical water molecule during enthalphy and entropy computations by MM-PSA ?
> my best regards,
> Jenk
> Jiri Sponer wrote: It has been done for example for quanine DNA quadruplexes,
> where monovalents are essential to stabilize this DNA
> It is possible and it works.
> Formation pathways of a guanine-quadruplex DNA revealed by molecular dynamics and thermodynamic analysis of the substates
> Author(s): Stefl R, Cheatham TE, Spackova N, Fadrna E, Berger I, Koca J, Sponer J
> Source: BIOPHYSICAL JOURNAL 85 (3): 1787-1804 SEP 2003
> Molecular dynamics simulations of guanine quadruplex loops: Advances and force field limitations
> Author(s): Fadrna E, Spackova N, Stefl R, Koca J, Cheatham TE, Sponer J
> Source: BIOPHYSICAL JOURNAL 87 (1): 227-242 JUL 2004
> best wishes, Jiri
> [ Charset ISO-8859-1 unsupported, converting... ]
> > Dear Amber community,
> >
> > I have such a complex system that one Na+ ion and two water molecules make a significant contribution to the stability of the complex and I personally wouldn't want to remove them during MMPBSA computations. I was wondering if any has succeeded including such essential ions and water molecules in MMPBSA computations. Can anyone please guide me on how this can be done and what outcome can be expected by MMPBSA for a complex system including ions and water molecules?
> >
> >
> > My best regards,
> >
> > Jenk
> >

   Cenk Andac, M.S., Ph.D. Student
 School of Pharmacy at
 Gazi University-Ankara Turkiye
  Address: Bandirma Sok. No:6
 Etiler, Ankara, 06330 Turkey
 Cell: +90-(536)-4813012

We won't tell. Get more on shows you hate to love
(and love to hate): Yahoo! TV's Guilty Pleasures list.
The AMBER Mail Reflector
To post, send mail to
To unsubscribe, send "unsubscribe amber" to
Received on Wed Mar 21 2007 - 06:07:17 PDT
Custom Search