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-- Pablo Englebienne, PhD Student, Moitessier research group Department of Chemistry, McGill University 801 Sherbrooke Street West Otto Maass bldg, room 206 H3A 2K6 Montréal, Québec, Canada Tel (514) 398-5501 Fax (514) 398-2382 "Progress is made by lazy men looking for easier ways to do things." - Robert A. Heinlein Lars Skjærven wrote: > Sorry for being imprecise.. > > Yes, water was added after adding the ions as recommended in the amber > manual. The number of counter ions added corresponds to the charge of > the protein so it is neutralized, ofcourse. :-) > > charge mol > addIons mol Na+ 250 > solvateBox mol TIP3PBOX 8 > > Lars > > On Dec 18, 2007 7:36 PM, Bill Ross <ross.cgl.ucsf.edu> wrote: > >>> We are simulating a protein of ~7500 residues using PME with pmemd. It >>> is quite negatively charged, so we added ~250 counter ions (Na+) with >>> the Leap (function addIons). The protein is really unstable, which is >>> not what we expected. >>> >> Did you add water too? >> >> Bill >> >> ----------------------------------------------------------------------- >> The AMBER Mail Reflector >> To post, send mail to amber.scripps.edu >> To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu >> >> > ----------------------------------------------------------------------- > The AMBER Mail Reflector > To post, send mail to amber.scripps.edu > To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu > ----------------------------------------------------------------------- The AMBER Mail Reflector To post, send mail to amber.scripps.edu To unsubscribe, send "unsubscribe amber" to majordomo.scripps.eduReceived on Sun Dec 23 2007 - 06:07:08 PST