AMBER Archive (2008)

Subject: AMBER: topology file

From: Giuseppe De Marco (g.de-marco_at_sussex.ac.uk)
Date: Mon Apr 14 2008 - 04:38:37 CDT

Dear Amber users,

I am trying to figure out how is defined the NONBONDED_PARM_INDEX in the
topology file of a 20-nucleotide RNA (the topology is generated using
tleap and leaprc.rna.ff99 ).

According to the description in the topology format it should be a
matrix (NTYPES*NTYPES), but is not very clear for me how the index
values are calculated.
By applying the formula : index = ICO(NTYPES*(IAC(i)-1)+IAC(j)) I don't
get he same values shown in the NONBONDED_PARM_INDEX.

In addition I would like to know if is possible to figure out the atoms
involved in the Lennard Jones interactions considering the following
parameters :

-ATOM_TYPE_INDEX
-NONBONDED_PARM_INDEX
-LENNARD_JONES_ACOEF
-LENNARD_JONES_BCOEF

Thanks in advance for any suggestion.

Giuseppe De Marco

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