[gmx-users] amidated terminus peptide simulation

Stanislaw Bobritsky beavered at gmail.com
Tue Sep 29 10:35:40 CEST 2009

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?

My protein consists of short alpha-helix, which undergoes some
conformational changes (helix bending and breaking) during the MD
simulation. And I have serious doubts about this MD correctness. May it be
an artifact of situation described above?

Thanks for help.

Stanislaw Bobritsky,
ChemBio Center, Taras Shevchenko National University, Kiev, Ukraine.
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