[gmx-users] Re: amidated terminus peptide simulation

Justin A. Lemkul jalemkul at vt.edu
Tue Sep 29 11:19:01 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.
>         -Justin
>     No the side chain is amidated in another way: since Tyr is
>     C-terminal residue, it is Tyr-CONH2 instead of Tyr-COO-.

The way you've written that is unclear.  If it is a C-terminal tyrosine, it 
should have a -COO- in the backbone, regardless of what you're doing to the side 

In any case, whatever charges you've assigned are somehow incorrect.  If you 
want more useful advice, provide the topology snippet pertaining to the charges 
on this modified residue.  Maybe someone can spot your problem.


>         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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