AMBER Archive (2007)

Subject: AMBER: polymer

From: Achuth Prabhu (achuthpnr_at_yahoo.co.in)
Date: Mon May 14 2007 - 07:55:12 CDT

hello all
   
   I am new to amber and i want to study the solvation
effects on a neutral polymer in water subject to
various temperatute conditions at a ph of 9. i have
created the top and crd files in leap but i am a bit
confused with sander input file for dynamics. i want
to calculate the change in the number of hydrogen
bonds - inter and intra - as well as the solvation
energies with respect to temperature and time. can
anybody tell me how to set the ph in the mdin file and
how to prepare the file?

thanks in advance

Achuth

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