AMBER Archive (2005)

Subject: Re: AMBER: van der waals parameters

From: Carlos Simmerling (carlos_at_ilion.bio.sunysb.edu)
Date: Wed Jan 12 2005 - 06:41:31 CST

IAC(I) is the atom nonbond type for atom I, IAC(J) is the type for atom
J. so, for atoms I and J, the rule listed for ICO gives the index
into the arrays for the actual nonbond parameter values.

===================================================================
Carlos L. Simmerling, Ph.D.
Associate Professor Phone: (631) 632-1336
Center for Structural Biology Fax: (631) 632-1555
Stony Brook University Web: http://comp.chem.sunysb.edu/carlos
Stony Brook, NY 11794-5115 E-mail: carlos.simmerling_at_stonybrook.edu
===================================================================

Monica Civera wrote:

>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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