AMBER Archive (2009)

Subject: [AMBER] R.E.D. help please

From: s. Bill (s_bill36_at_yahoo.co.uk)
Date: Wed Jul 15 2009 - 09:11:46 CDT

Dear AMBER
I need really a help. I am a new user in AMBER and i got completely confused in generating a non-standard residue charge.
According to R.E.D. the charge is changing by changing the molecular orientation, so I should define in R.E.D. which orientation I used in generating the charge, as well as, I can specify more than one orientation (and this is recommended by R.E.D.). So, now, I am using Gaussian in calculation charge (pop=Mk). How can I specify the orientation during calculating the molecule's charge? Gaussian uses an internal algorithm for molecular orientation.
Also, should I recalculate the molecule's charge by using Gaussian for different orientations?
and in this case, how can I emerge the different Gaussian outputs for different orientation? or I calculate it once, and then specify different orientation in R.E.D.? and according to which principle, atoms used in specify orientation are chosen? i.e. which three atoms can I use for orientation specification?
PLEASE, any one direct me and answer these simple questions?
Thanks in advance
bill

      
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