On Wed, 2014-05-21 at 16:14 +0200, Rossen Apostolov wrote:
> Hi Jason,
>
> I found the issue.
>
> At the time of porting, the implementation has been validated against
> AMBER 8 and the results have matched very precisely the GROMACS ones.
>
> Looking at the sources, AMBER 8 has in amber8/dat/leap/cmd/leaprc.ff03:
>
> ..snip..
> loadOff all_aminoct94.lib
> loadOff all_aminont94.lib
> ..snip..
>
> This has been updated in later Amber versions. E.g. in the latest AMBER
> 14 amber14/dat/leap/cmd/leaprc.ff03.r1 has:
>
> ..snip..
> loadOff all_aminoct03.lib
> loadOff all_aminont03.lib
> ..snip..
>
> I will update those in Gromacs too.
Ah... Well that could explain my ignorance. Looking through the git
log, the "new C- and N-terminal ff03 files" were added back in early
2008 (before I even started my graduate studies). This would have been
first seen in the Amber 10 release if I have my timeline straight.
Thanks!
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Wed May 21 2014 - 08:00:02 PDT
