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
>
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>
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Received on Thu Jun 14 2012 - 12:30:03 PDT
