On Fri, May 17, 2013, Amparo Garcia Lopez wrote:
>
> Now my only thought is why they gave the
> same name (ff10) to two different force fields (with and without the chi
> correction),
You have a legitimate complaint here, but let me explain a bit:
AmberTools1.4 (released in April, 2010) does not document "ff10", but
lists leaprc.ff99bsc0 as the relevant force field file in the Users'
Manual. However, the tar file apparently (and inadvertently) had "ff10"
files (which were being used internally).
We added the OL3 chi corrections in November, 2010; soon after than, we
updated the atom and residue names to the new PDB standard (hence the change
from all_nucleic* to nucleic*. Both of these changes were incorporated
into AmberTools1.5 (released in April, 2011), where for the first time we
documented the "ff10" force field. We failed to realize that there had been
some earlier ff10 files in the 1.4 release, and hence did not worry about any
such conflicts.
[To further complicate things, the header for parm10.dat was not updated to
inlcude a reference to OL3 until even later.]
I apologize for the confusion this has caused. Note that current users (with
AmberTools13, or AmberTools12 with all updates applied) should use
leaprc.ff12SB -- see Chapter 2 of the AmberTools13 Reference Manual.
...dac
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Received on Fri May 17 2013 - 06:00:04 PDT
