On Mon, Sep 05, 2016, Mark Abraham wrote:
>
> Thanks for the response. It seems that amber03 had LYN charge parameters
> that changed at some point in the AMBER program prep files, perhaps as a
> fix. But it is hard for me to find the reason for the change, to know
> whether e.g. the GROMACS implementation is wrong because we copied the old
> version and haven't known to stay in sync. This apparently does affect LYN
> in amber03, but maybe other things got fixed in AMBER alongside that fix,
> and this would also need attention in GROMACS. If there was a publicly
> readable source code repository then I could search it, but I don't think
> that exists.
In July of 2004(!), there was a commit to the all_amino03.lib file regarding
the LYN charges. The ones originally there were copied from the ff94 force
field, and had not been updated to reflect the "ff03" way of obtaining
charges. The 2004 commit provided the "correct" ff03 charges for LYN.
There haven't been any further changes to the LYN charges.
[FWIW: the only other change I see is a change to the HIP charges in Nov.
2005--logs are unclear about why this change was made. As Carlos suggested,
you might want to try to contact Yong Duan directly.
...hope this helps....dac
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Received on Mon Sep 05 2016 - 18:00:02 PDT
