Hi George,
Well, having counter ions to get a neutral charge depends on whether you
want to use explicit solvent (with periodic boundary conditions) or
implicit solvent. Without periodic boundaries, you don't need charge
neutralisation.
Benefit of implicit solvent is probably that you may see the conformational
change you want more quickly. Downside may be that the dynamics you see is
less physically realistic.
In any case, if you don't do constant pH MD, you don't want to be using AS4
as residue name (I believe).
To specify a protonated ASP, call it ASH (as well as GLH for protonated
GLU).
Hope this helps,
Marc
On 14 June 2012 21:10, George Tzotzos <gtzotzos.me.com> wrote:
> Jason, Marc,
>
> Many thanks. I had written to the list earlier regarding the type of
> simulation I'm trying to run.
>
> On May 11, I wrote "The protein I'm dealing with has "lid" over the
> binding cavity which is assumed to open at acidic pH releasing the bound
> ligand."
>
> Initially, I intended to run constant pH MD.
>
> Jason replied "Then this is not a constant pH MD".
>
> Whereas Marc suggested
>
> "Why not determine what the protonation states of your residues would be at
> pH=4.0 and run standard MD (not constant pH MD), at least as an initial
> test. Presumably, many of the histidines would be doubly protonated, and
> perhaps
> some glutamate / aspartates as well."
>
> This is precisely, what I'm now trying to do.
>
> Given your answers, the question is whether charge neutralisation is
> needed.
>
> Once again, many thanks for the invaluable help.
>
> George
>
>
> On Jun 14, 2012, at 9:37 PM, Jason Swails wrote:
>
> > A piece of warning here -- do NOT add ions. Constant pH simulations only
> > work in implicit solvent, so neutralizing ions don't belong here.
> >
> > HTH,
> > Jason
> >
> > On Thu, Jun 14, 2012 at 3:27 PM, Marc van der Kamp <
> marcvanderkamp.gmail.com
> >> wrote:
> >
> >> Dear George,
> >>
> >> As for 'normal' MD simulations, you will need to load parameters for
> ions
> >> in addition to your force field.
> >> The reason is that the parameters differ depending on the water model
> you
> >> use, so for TIP3P for example you need to do:
> >>
> >> loadamberparams frcmod.ionsjc_tip3p
> >>
> >> This has been outlined on the mailing list several times, and I think is
> >> mentioned elsewhere (manual?, recent tutorials) too.
> >>
> >> Hope this helps,
> >> Marc
> >>
> >> On 14 June 2012 20:10, George Tzotzos <gtzotzos.me.com> wrote:
> >>
> >>> Dwight
> >>>
> >>> Thank you, much appreciated.
> >>>
> >>> I did as you suggested.
> >>>
> >>> The total charge of my COMPLEX is 2.000
> >>>
> >>> I added Cl- (addions COMPLEX Cl- 0) and solvated the box.
> >>>
> >>> When I tried to save the parameter file, I got
> >>>
> >>> For atom: .R<Cl- 127>.A<Cl- 1> Could not find type: Cl-
> >>> For atom: .R<Cl- 128>.A<Cl- 1> Could not find type: Cl-
> >>> Parameter file was not saved.
> >>>
> >>> Looking at leaprc.constph I see that atom Type Cl- is defined.
> >>>
> >>> Any suggestions for this.
> >>>
> >>> Best regards
> >>>
> >>> George
> >>>
> >>>
> >>> On Jun 14, 2012, at 6:43 PM, Dwight McGee wrote:
> >>>
> >>>> Hi,
> >>>>
> >>>> The error was printed because you were using the wrong force field.
> You
> >>>> should load *leaprc.constph* instead for Constant pH simulations.
> >>>>
> >>>> On Thu, Jun 14, 2012 at 11:52 AM, George Tzotzos <gtzotzos.me.com>
> >>> wrote:
> >>>>
> >>>>> I am trying to generate a topology file for a low pH MD simulation.
> >>>>>
> >>>>> I renamed the HIS, GLU and ASP residues in the starting PDB file to
> >> HIP,
> >>>>> GL4, AS4.
> >>>>>
> >>>>> For tleap I'm using leaprc.ff99SB
> >>>>>
> >>>>> Loading my protein.pdb file I get, for example,
> >>>>>
> >>>>> Unknown residue: AS4 number: 5 type: Nonterminal
> >>>>> etc.
> >>>>>
> >>>>> Trying to save the topology file, generates FATAL errors of the type
> >>>>>
> >>>>> FATAL: Atom .R<AS4 7>.A<N 1> does not have a type.
> >>>>>
> >>>>> I checked the mail archive and couldn't find anything that could help
> >> me
> >>>>> solve this problem.
> >>>>>
> >>>>> Your help will be appreciated
> >>>>>
> >>>>> Best regards
> >>>>>
> >>>>> George
> >>>>> _______________________________________________
> >>>>> AMBER mailing list
> >>>>> AMBER.ambermd.org
> >>>>> http://lists.ambermd.org/mailman/listinfo/amber
> >>>>>
> >>>>
> >>>>
> >>>>
> >>>> --
> >>>> T. Dwight McGee Jr.
> >>>> Quantum Theory Project
> >>>> University of Florida
> >>>> Graduate Student
> >>>> dwight.mcgee.gmail.com
> >>>>
> >>>> "Problems cannot be solved at the same level of awareness that created
> >>>> them."
> >>>> Albert Einstein
> >>>> _______________________________________________
> >>>> AMBER mailing list
> >>>> AMBER.ambermd.org
> >>>> http://lists.ambermd.org/mailman/listinfo/amber
> >>>
> >>> _______________________________________________
> >>> AMBER mailing list
> >>> AMBER.ambermd.org
> >>> http://lists.ambermd.org/mailman/listinfo/amber
> >>>
> >> _______________________________________________
> >> AMBER mailing list
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> >> http://lists.ambermd.org/mailman/listinfo/amber
> >>
> >
> >
> >
> > --
> > Jason M. Swails
> > Quantum Theory Project,
> > University of Florida
> > Ph.D. Candidate
> > 352-392-4032
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
>
>
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Received on Thu Jun 14 2012 - 13:30:04 PDT
