On Tue, Sep 24, 2013, Adam wrote:
>
> While double checking to make sure I had set my system up properly, I was
> looking through the charges and realized that the charge on protonated
> histidine inside of Amberff03 did not add up to +1
I think I see what may be the problem, but a lot depends on exactly what you
mean by "inside of Amberff03". The leaprc.ff03.r1 file (which kind of defines
revision "r1" of ff03, loads all_amino03.lib, which has the correct charges.
In turn, the "lib/ff03.cmd" file creats lib/all_amino03.lib from
prep/all_amino03.in. The latter file has correct HIP charges, but also
has some typos that make some things look wrong. The charges in the prep
file that are on the same line as the atom names are actually ignored:
the charges in the CHARGE block below are the ones that are actually used.
In the case of HIP, the latter are correct but the former are incorrect.
So, under normal tleap usage, the Amber ff03 charges should be correct.
Other programs (or humans) reading the all_amino03.in file could easily be
confused. I will fix the charges and post an update soon.
(Of course, there should not be two places where charges for the same residue
are given, since that is just asking for things to get out of sync, as
happened here. All I can say is that the prep format goes way back to late
1970's. Originally, there was just a CHARGE block. Later, someone (I'm
pleading both ignorance and innocence here) noted that it would be easier to
read the charges if they were on the same line as the coordinates. But I'm
guessing that the CHARGE block was retained in some attempt at backward
compatibility.)
Thanks for the report.
...dac
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Received on Tue Sep 24 2013 - 19:00:03 PDT
