AMBER Archive (2000)

Subject: PMF and PME with DNA

From: David Bosch (david_at_milu.uab.es)
Date: Mon Nov 13 2000 - 03:51:47 CST

Dear AMBER users,

Some time ago we posted a message to this AMBER list concerning to the use of
PME during a perturbation run of a DNA system. We are aware of the bugfix.16
about PME used on SGI machines, so we implemented it. However, when running the
PMF calculation with PME turned on, the system coordinates becomes a nonsense
with clashes, base frayings, etc. Moreover, what it is most striking is that the
program does not complain at all and that the free energies obtained are not as
unbelievably high at all.

Please, any help from anybody that has successfully performed PMF calculations
with PME will be vey wellcome.

Thanks for your attention,

David Bosch, Ph. D student
lab. Medicina Computacional
Facultat de Medicina
Universitat Autònoma de Barcelona
08193 Bellaterra
CATALUNYA