AMBER Archive (2005)

Subject: AMBER: van der waals parameters

From: Monica Civera (monica.civera_at_unimi.it)
Date: Wed Jan 12 2005 - 05:42:53 CST

dear users,
does any of you can explain to me the rule to calculate the index ICO in the
topology file?

In Amber8' Manual I found:

' FORMAT(12I6) (ICO(i), i=1,NTYPES*NTYPES)
  ICO : provides the index to the nonbon parameter
           arrays CN1, CN2 and ASOL, BSOL. All possible 6-12
           or 10-12 atoms type interactions are represented.
           NOTE: A particular atom type can have either a 10-12
           or a 6-12 interaction, but not both. The index is
           calculated as follows:
             index = ICO(NTYPES*(IAC(i)-1)+IAC(j))
           If index is positive, this is an index into the
           6-12 parameter arrays (CN1 and CN2) otherwise it
           is an index into the 10-12 parameter arrays (ASOL
           and BSOL).'

What is the value of th J index?

thanks in advance

monica

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