<blockquote><blockquote style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;" class="gmail_quote"><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
Hello everyone again, I have one more question for today.<br>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. <br>
<br>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 <i>"System has non-zero total charge: -2.700006e-01". </i>Even after ions added.<i> </i>How much critically is it? What should I do? Or it is unimportant?<br>
</blockquote></blockquote><div><blockquote style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;" class="gmail_quote"><pre>You have a non-integral charge in a system that should be integral. That is a <br>
problem. Occasionally, small rounding errors occur, but I would say that is <br>certainly not the case here.<br><br>Something about the charges you've used is wrong. Is the side chain amidated in <br>some way, or the backbone? If it's the backbone, Gromacs can deal with this <br>
automatically in pdb2gmx.<br><br>-Justin</pre></blockquote> <br>No
the side chain is amidated in another way: since Tyr is C-terminal residue, it is Tyr-CONH2 instead of Tyr-COO-.<font color="#888888"><br><br></font><blockquote style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;" class="gmail_quote">
Stanislaw Bobritsky,<br><font color="#888888"></font>ChemBio Center, Taras Shevchenko National University, Kiev, Ukraine.</blockquote></div></blockquote><div class="gmail_quote"><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
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