AMBER Archive (2009)
Subject: [AMBER] rdparm bug?
From: Paul Mortenson (P.Mortenson_at_astex-therapeutics.com)
Date: Tue Jul 07 2009 - 11:29:44 CDT
I think I may have found a bug in rdparm. I have tried to use it to
remove a single water from a box of waters, but the prmtop file
generated seems to get the two equilibrium bond lengths for TIP3P the
wrong way round (or equivalently, is labelling the bonds in the system
incorrectly). When I then use this prmtop file to calculate the energy
of the modified system, the calculated bond energy is enormous (~450000
kcal/mol). If I hack the prmtop file and swap the two equilibrium bond
lengths around, I get a much more sensible answer, which as expected is
close to the energy of the original system. I have attached a trivial
example illustrating this.
I'm using rdparm from a fully patched version of AmberTools 1.2, and
sander from AMBER 9. I'm running on CentOS Linux v4.6.
Thanks in advance for any help, and please let me know if I can provide
any more information.
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