From: Him Shweta <shwetahim.gmail.com>
Date: Tue, 29 Jul 2014 13:07:39 +0530

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.



       1 -1 -1 3

I have attached the topology file of single water molecule.

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Received on Tue Jul 29 2014 - 01:00:02 PDT
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