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
-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber.scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu
Received on Fri Apr 18 2008 - 21:19:12 PDT
