AMBER Archive (2008)

Subject: AMBER: Where is ICO read from the ix array?

From: Brad Lambeth (
Date: Mon Jul 21 2008 - 14:49:44 CDT

I'm looking for the place in the sander code where ICO is assigned based on
ix. I see that the non-bonded parameter index is read in rdparm.f to the
array ix, but I can't find where ICO is defined after that. Appended below
is my previously unanswered inquiry about 10-12 and 6-12 interaction
parameters, which is the reason for my question this time. I'm convinced
that sander is reading my ASOL and BSOL coefficients correctly, but I'm
curious as to what it's reading for ICO based on my prmtop.

Brad Lambeth
Graduate Student
Rice University

---------- Forwarded message ----------
From: Brad Lambeth <>
Date: Sat, Jul 12, 2008 at 7:20 PM
Subject: Atom type with 10-12 and 6-12 interactions in Amber9

The amber file formats document
<>states that an atom type can
have either a 10-12 interaction or a 6-12
interaction, but not both. What is the reason for this limitation? Is
there a specific portion of the code that makes this impossible?

For my system, I have 5 atom types; 1 atom type interacts with all the
others with a 6-12 potential, while the other 4 atom types interact with
each other with the 10-12 potential. This means those 4 atom types have
10-12 interactions and 6-12 interactions. When I generate my prmtop and
analyze it with rdparm, I cannot get it to read the coefficients correctly
based on ICO and the ASOL and BSOL input. I have tried many different ways
of assigning ICO without success.

I noticed that the rdparm program uses c code that seems independent of the
code used for sander. Is this issue only part of the rdparm program, or
does it also apply to sander as well?

Brad Lambeth
Graduate Student
Rice University

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