Hello everyone again, I have one more question for today. >> I try to perform a simulation of small peptide (37 residues). When I set >> up a system with COO- terminus, the total charge is +2, so I add 2 counter >> ions and have no problem. >> >> But this protein has amidated C-terminus in nature. I wrote a topology for >> amidated terminal residue (Tyr-CONH2 in my case: charges were taken from Gln >> amide group), and the system successfully passed minimization and positional >> restraint equilibration stages (3 Cl- were added to make charge neutral). >> But the fact making me uneasy is *"System has non-zero total charge: >> -2.700006e-01". *Even after ions added.* *How much critically is it? What >> should I do? Or it is unimportant? >> > You have a non-integral charge in a system that should be integral. That is a > problem. Occasionally, small rounding errors occur, but I would say that is > certainly not the case here. > > Something about the charges you've used is wrong. Is the side chain amidated > in > some way, or the backbone? If it's the backbone, Gromacs can deal with this > automatically in pdb2gmx. > > -Justin > > No the side chain is amidated in another way: since Tyr is C-terminal residue, it is Tyr-CONH2 instead of Tyr-COO-.
Stanislaw Bobritsky, > ChemBio Center, Taras Shevchenko National University, Kiev, Ukraine.
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