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? 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.
_______________________________________________ gmx-users mailing list [email protected] http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [email protected]. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
