[gmx-users] amidated terminus peptide simulation

Justin A. Lemkul jalemkul at vt.edu
Tue Sep 29 10:49:56 CEST 2009

Stanislaw Bobritsky wrote:
> 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.


> 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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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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