AMBER Archive (2008)

Subject: AMBER: Atom type with 10-12 and 6-12 interactions in Amber9

From: Brad Lambeth (bradlambeth_at_rice.edu)
Date: Sat Jul 12 2008 - 19:20:09 CDT

The amber file formats document
<http://amber.scripps.edu/formats.html>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?

Thanks,
Brad Lambeth
Graduate Student
Rice University

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