AMBER Archive (2007)

Subject: Re: AMBER: Work with constand pH

From: tri nam Vo (mouseelephant2002_at_yahoo.com)
Date: Thu Apr 26 2007 - 22:37:53 CDT

Dear Myunggi,
  I'm still confused. The manual just say too simple, is there any tutorial which more detail?(I've just read the manual amber8.pdf part 5.19)
  I've some questions: should we include cipn file when run minimization by -cpin flag ? In that case, should we set value for icnstph and solvph parameters in min.in file?
  And which value is suitable for nstlim? My protein have 175aa.
  Thanks a lot.

Myunggi Yi <myunggi_at_gmail.com> wrote:
  As you have read, you'll use GB implicit solvent model.
Don't solvate (neutralize) your protein, and follow the example in the manual.

       
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