Dear Amber Users,
In the general topolgy file format for amber topology file, evertything is
clear except the %FLAG NONBONDED_PARM_INDEX.
I dont understand how indexing is done for Nonbonded terms which uses the
following relation:
index = ICO(NTYPES*(IAC(i)-1)+IAC(j))
For understanding purpose i made a topology file for single water molecule,
but i could not understand the nonbonded index term that from where the
values 1, -1, -1, 3 came and what is its meaning.
%FLAG NONBONDED_PARM_INDEX
%FORMAT(10I8)
1 -1 -1 3
I have attached the topology file of single water molecule.
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Tue Jul 29 2014 - 01:00:02 PDT
