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 - 18:00:02 PST
