Date: Wed Nov 15 2006 - 11:34:32 CST
I am trying to build a POPS molecule from a POPE lipid to simulate a
membrane with NAMD. In the topology file file of Charmm, POPE is
included. Since the difference between POPS and POPE is that the first
has got a "COO-" instead an H, I have thought that I could delete the
H atom from POPE and substituing it by a CTER.
My doubt is about charges: where does go the charge of the "H" I am
eliminating? To the carbon of the old POPE, or half to the POPE and
half to the CTER? Since the CTER is supposed not to be joined to
anyone in the topology file, I suppose the entire charge of the H left
will go to the carbon of the old POPE, am I right?
Thank you very much for your help in advance!!
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