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From: Investigador Química <investigacion.faq.gmail.com>

Date: Sat, 22 Aug 2015 16:38:37 -0400

Dear Prof. Roitberg,

Thank you for your time and advise. You were right about the number of

ions. Now I am trying to fit the charges using RESP on AMBER.

Best regards

2015-08-20 12:41 GMT-04:00 Adrian Roitberg <roitberg.ufl.edu>:

*> I am also confused as to why your TOTAL charge is not the same as the
*

*> sum of H and G charges... Unless you are changing the number of ions,
*

*> which would make it very hard to compute what you are trying to compute.
*

*>
*

*> adrian
*

*>
*

*>
*

*> On 8/20/15 10:09 AM, Investigador Química wrote:
*

*> > Dear Jason, thank you for your kind and clear explanation.
*

*> > You are right. For the three isolated and solvated systems generated
*

*> using
*

*> > "solvateoct TIP3PBOX 11" we have:
*

*> >
*

*> > Box (x=y=z) triangulated 3-points waters sum of
*

*> charges
*

*> >
*

*> > H-G 64,477 6598 -0.99950000
*

*> > H 51,248 3254 -0.16460000
*

*> > G 37,612 1321 -0.03280000
*

*> >
*

*> > My problem is how can I run the simulations with the water counts exactly
*

*> > matched between the bound and unbound simulations?
*

*> >
*

*> > In AMBER tutorial 21 the following values are used for
*

*> > water_tleap.in: solvatebox structure TIP3PBOX 16.50 iso
*

*> > b2_tleap.in: solvatebox guest TIP3PBOX 13.16 iso
*

*> > CB7_tleap.in: solvatebox host TIP3PBOX 10.18 iso
*

*> > CB7_b2_tleap.in: solvatebox b2host TIP3PBOX 9.91 iso
*

*> >
*

*> > and manually they removed waters over 1500.
*

*> >
*

*> > In my case I do'nt know how to choose the appropriated number of waters
*

*> or
*

*> > the numbers of the
*

*> > TIP3PBOX Nr? iso
*

*> >
*

*> > Could you please help me?
*

*> >
*

*> > Thank you for your help and time!
*

*> >
*

*> > Best regards
*

*> >
*

*> > 2015-08-19 11:18 GMT-04:00 Jason Swails <jason.swails.gmail.com>:
*

*> >
*

*> >> On Wed, 2015-08-19 at 10:43 -0400, Investigador Química wrote:
*

*> >>> Dear Jason, thank you for your kind explanation. I recognize my first
*

*> >>> question was not fortunate. Please let me to explain my question.
*

*> >>> If I have the Etot for a host H, for a guest G and for the complex
*

*> H-G, I
*

*> >>> can calculate the interaction energy as E= E(complex H-G) - E(H) -
*

*> E(G),
*

*> >>> isn't?.
*

*> >> Loosely speaking, yes. However, there are countless ways to do this
*

*> >> wrong. For example, if the sum of the host and guest systems do not
*

*> >> have exactly the same number (and *kind*) of atoms and molecules as the
*

*> >> bound complex, then this energy difference is completely arbitrary (and
*

*> >> meaningless). After all, energy is extensive, so you can tune the
*

*> >> interaction energy to be any value you want by simply adding solvent to
*

*> >> either the bound or unbound species and not to the other.
*

*> >>
*

*> >> There are many ways to compute the interaction energies (MM/PBSA is one
*

*> >> example, and the linear response theory/linear interaction energy is
*

*> >> another). Whichever you use must make sure that the only energies that
*

*> >> are left after taking the difference are the interactions between the
*

*> >> atoms in the host and the atoms in the guest.
*

*> >>
*

*> >>> If I get the energies for the three entities using solvateoct and
*

*> >>> TIP3PBOX from 8 to 11 each time (for the three entities each time) I
*

*> get
*

*> >>> different interaction energies. Should the interaction energy best
*

*> value
*

*> >> be
*

*> >>> the lower one?
*

*> >> No. This is known as the variational principle and is common in QM
*

*> >> calculations (i.e., a method is variational if a lower energy *ensures*
*

*> >> a better approximation of the true wavefunction). Force fields are
*

*> >> *certainly* not variational, and even variational QM Hamiltonians won't
*

*> >> be variational in an interaction energy calculation like this.
*

*> >>
*

*> >>> How can I know that, if I have no experimental values to
*

*> >>> compare with?
*

*> >> You can't. You have to use your judgement and rationalize which model
*

*> >> for computing the interaction energy is the best.
*

*> >>
*

*> >>> For instance these were the values I got when running 3 ns
*

*> >>> of MD equilibration according to AMBER tutorial 1 section 5:
*

*> >> 3 ns is a very short simulation.
*

*> >>
*

*> >>> box 8: E= -11067 kcal/mol
*

*> >>> box 9: E= -10363 kcal/mol
*

*> >>> box 10: E= -8276 kcal/mol
*

*> >>> box 11: E= -6485 kcal/mol
*

*> >> These are huge differences. You haven't described exactly how you are
*

*> >> computing the interaction energies, but this looks to me like the fewer
*

*> >> particles you use, the lower your energy gets. This can happen if you
*

*> >> have 3 separate systems (H-G, H, G) each independently solvated and you
*

*> >> take the energy of each one and subtract them. With an 11 A buffer, H+G
*

*> >> will have a *lot* more water-water interactions between the two systems
*

*> >> than the HG system compared with, say, an 8 A buffer. Which means that
*

*> >> the total interaction energy will *appear* lower, because your
*

*> >> difference includes more interactions than *just* those between your
*

*> >> host and guest.
*

*> >>
*

*> >> Possible differences arising from box size effects will be related to
*

*> >> periodic images interacting with each other, different conformational
*

*> >> ensembles caused by either incomplete sampling or periodicity artifacts,
*

*> >> and some net charge effects if you have a non-neutral unit cell with
*

*> >> periodic boundary conditions. However, I wouldn't expect any of those
*

*> >> effects (excluding incomplete sampling) to be larger than ~10 kcal/mol,
*

*> >> let alone up to 5000!
*

*> >>
*

*> >> HTH,
*

*> >> Jason
*

*> >>
*

*> >> --
*

*> >> Jason M. Swails
*

*> >> BioMaPS,
*

*> >> Rutgers University
*

*> >> Postdoctoral Researcher
*

*> >>
*

*> >>
*

*> >> _______________________________________________
*

*> >> AMBER mailing list
*

*> >> AMBER.ambermd.org
*

*> >> http://lists.ambermd.org/mailman/listinfo/amber
*

*> >>
*

*> >
*

*> >
*

*>
*

*> --
*

*> Dr. Adrian E. Roitberg
*

*> Professor.
*

*> Department of Chemistry
*

*> University of Florida
*

*> roitberg.ufl.edu
*

*> 352-392-6972
*

*>
*

*>
*

*> _______________________________________________
*

*> AMBER mailing list
*

*> AMBER.ambermd.org
*

*> http://lists.ambermd.org/mailman/listinfo/amber
*

*>
*

Date: Sat, 22 Aug 2015 16:38:37 -0400

Dear Prof. Roitberg,

Thank you for your time and advise. You were right about the number of

ions. Now I am trying to fit the charges using RESP on AMBER.

Best regards

2015-08-20 12:41 GMT-04:00 Adrian Roitberg <roitberg.ufl.edu>:

-- Área de Software Investigación Facultad de Química Universidad de Santiago de Chile _______________________________________________ AMBER mailing list AMBER.ambermd.org http://lists.ambermd.org/mailman/listinfo/amberReceived on Sat Aug 22 2015 - 14:00:06 PDT

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