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
chain.
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.
-Justin
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
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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