On Thu, Jun 14, 2012, George Tzotzos wrote:
>
> 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.
Please see Section 2.11 ("Ions") in the AmberTools12 Reference Manual.
You need to issue the command "loadAmberParams frcmod.ionsjc.<watermodel>" to
choose the ion parameters that go along with the water model you have chosen.
[Although the manual is correct, it is really too bad that no example is
given!]
More disturbing, however, is the fact that you are loading leaprc.constph for
a solvated simulation. Unless I am missing something( Jason???) Amber12 does
*not* support constant pH in explicit solvent.
If you wish to run a low pH (not constant pH) simulation in explicit solvent,
you need to use the ASH and GLH residues for asp and glu (not AS4 and GS4).
[Someone please correct me if I am wrong here! I know there is development
work going on towards running constant pH in explicit solvent, but I don't
think this capability is in Amber12.]
....dac
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Received on Thu Jun 14 2012 - 13:30:04 PDT
