You can technically run MD, but I'd be worried about the residue(s) you've
just made. What pmemd (or pmemd.cuda) will do is tell you "Sum of charges
from parm topology file = 0.37999999." And, since that's greater than 0.01,
it will say "Assuming uniform neutralizing plasma." This means that it's
going to lean on the Ewald tinfoil boundary conditions, setting the first
Fourier frequency value explicitly to zero. It's not that the system
dynamics is necessarily bad if you have +1, or even -3 proton units' excess
charge on the system. If you think that it resonates with protons in the
surrounding water to accumulate that partial charge in a mean sense, this
is actually not a bad idea--the problem is that all of the other residues
are neutral or of integer charge, so the rest of the model isn't ready to
swing the way of your new residues.
Dave
On Sun, Nov 11, 2018 at 7:43 AM maryam azimzadehirani <
maryamai1988.gmail.com> wrote:
> Dear Amber users,
> I have generated a glycosylated protein using xleap. I am using AMBER tools
> 17 and I have sourced the ff14SB for protein atoms and glycam forcefield
> for the glycans. All glycosylated Asns are renamed to NLN. However I got
> this warning from the leap:
> *The unperturbed charge of the unit: -0.388000 is not integral*
> can I proceed for MD with such warning?
> thanks in advance
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>
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Received on Sun Nov 11 2018 - 23:30:03 PST
