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pdb2psf ; NaCl ; polyelectrolytes ; polylysin

Eugene Leitl ui22204 at mail.lrz-muenchen.de
Sun Apr 12 13:51:48 EST 1998


I am an molecular modeliing novice, doing MD of heavily hydrated (using
Solvate) polylysin. However, so far I cannot generate counterions. I would
like to have bromides, but I'd settle for chlorides. The problems: 

1) which parameter files do I need? There seems no chloride parameter files
coming with X-PLOR(online) Version 3.851 distribution. 

2) to avoid the bogus 999 .pdb generated coordinate problem, I naively think
that adding the chlorides into the .pdb, rereading it, then dumping the new
.psf sufficeth. Is this true? If yes, anybody got some illustrating X-PLOR
script sources? 

Thanks a lot,
Eugene Leitl

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