amber-developers: Extra Points Calculation

From: Lachele Foley <>
Date: Wed, 05 Nov 2008 11:04:45 -0500

Back in the days of Amber 7 & 8, a member of our group worked on EP parameters for sugars. In order to do that, she had to change the code and recompile sander. I would like to use her parameters, but the current code won't work. I think the changes she had to make never got incorporated into the general code.

I've attached a pdf describing the changes she made to versions 7 & 8. I looked at the relevant bits of code in more recent versions, and it has changed enough that I am not comfortable guessing equivalent changes. Is it possible to make similar changes to the current tree (and maybe for Amber 10 as well)?

I think the basic problem in the un-changed code is that there are more extra pairs in sugars than what the code expects in a typical residue. When I try to run, the error message in the output file says:

 fill_bonded: max14 exceeded!!

The output file containing this message is included in the tarball and has an obvious name. This output is from a run on a 32-bit machine running RHEL 4u4.

To further assist, the tarball contains a complete set of input files, along with the output I was able to get from runs using recompiled versions of Amber 7 & 8 (they behave essentially the same) along with that one output file from Amber 11.

More notes about running with the recompiled Amber 7 & 8:

* Minimization seems to work fine. (output in tarball was run on the 32-bit machine) The restart file looks pretty sane.

* Constant volume heating hangs. It seems to start fine, but just hangs. I have also attached the output file from that simulation. The *.e2* files, showing output reported by PBS, are probably informative. These particular complaints are from an Itanium2 system, but those on a xeon (32-bit) look similar. I can send those as well if you're interested.

I'm sure you need some bit of information I didn't think of. Just let me know.

:-) Lachele
B. Lachele Foley, PhD '92,'02
Assistant Research Scientist
Complex Carbohydrate Research Center, UGA

Received on Fri Dec 05 2008 - 10:52:07 PST
Custom Search