AMBER Archive (2005)

Subject: AMBER: AMBER topology file format

From: santanu chatterjee (santanu_c10_at_yahoo.co.in)
Date: Mon Aug 22 2005 - 04:18:18 CDT

Hi,
  I am a newbie in AMBER. I need to write code to read
AMBER topology format for biomolecules. I am following
the format specification given at this page:
http://amber.scripps.edu/formats.html.

  I am not very clear how IAC and ICO is being used to
find out the appropriate lennard-jones parameters from
CN1, CN2, ASOL and BSOL.

  The formula is given as the following:
index=ICO(NTYPES*(IAC(i)-1)+IAC(j)). What is meant by
i and j in this formula? Are these just the atom
numbers or the atom types? I would appreciate if
anyone could clarify this.

Thanks in advance,
san

        

        
                
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