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
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
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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