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
> >
> _______________________________________________
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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
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Received on Thu Jun 14 2012 - 13:00:03 PDT
