Hi,
I am following the amber tutorial on membranes, and I am puzzled by the charge of the membrane itself. I am buildling a system with a protein, no problem with that but when I upload the membrane alone as a .pdb that came out from charmm GUI, I get the splitting warning, that I ignore. And I can of course to save the amber prmtop and inpcrd with the protein. But the charge command gives me a 0.
My question is about the charge and addions commands, the charge on the membrane alone is zero!!, which is not possible of course. How should I deal with the charge of the membrane. I know from what it came out from CHARMM GUI, that with 0.15 molar of KCl Charmm added 14 K+ ions. Should I add them? How?
Thanks a lot in advance,
Fabian
Fabian Glaser
Head of the Structural Bioinformatics section
Bioinformatics Knowledge Unit - BKU
The Lorry I. Lokey Interdisciplinary Center for Life Sciences and Engineering
Technion - Israel Institute of Technology, Haifa 32000, ISRAEL
fglaser at technion dot ac dot il
Tel: +972 4 8293701
http://bku.technion.ac.il
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Received on Mon Mar 28 2016 - 02:30:03 PDT
