[gmx-users] Re: amidated terminus peptide simulation

Stanislaw Bobritsky beavered at gmail.com
Tue Sep 29 11:03:18 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?
> 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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