Dear David,
Thank you for your suggestions.
The problem has been solved.
Best regards,
Ya
On Tue, Dec 9, 2014 at 9:30 AM, David A Case <case.biomaps.rutgers.edu>
wrote:
> On Tue, Dec 09, 2014, Ya Gao wrote:
> >
> > I want to perform a simulation with amoebapro13 force field and amoeba
> > water model using pmemd.amoeba in amber14.
> >
> > The system is myoglobin, which is placed in a cubic water box using
> > solvatebox with 2 Cl- ions to neutralize the system.
>
> Just to add to what Jason said: Check what the ions look like in your
> input
> pdb file. I think they should look like this:
>
> ATOM 1969 Cl- Cl- 130 19.451 15.906 -29.108 1.00 0.00
>
> If you have something differernt, try the above. If not, a small test case
> would be very helpful.
>
> ...thanks....dac
>
>
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Received on Mon Dec 08 2014 - 22:00:03 PST
