On Sat, Jun 04, 2016, 163邮箱 wrote:
>
> Checking parameters for unit 'complex'.
> Checking for bond parameters.
> Could not find bond parameter for: NA - FE
> Checking for angle parameters.
> Could not find angle parameter: CW - NA - FE
> Could not find angle parameter: H - NA - FE
> Could not find angle parameter: NA - FE - NP
> Could not find angle parameter: NA - FE - NO
> Could not find angle parameter: NA - FE - NP
> Could not find angle parameter: NA - FE - NO
> Could not find angle parameter: CR - NA - FE
You are doing something very odd here: are you sure the histidine is a HID,
not HIE (which is the default if you just list it as "HIS" in the pdb file.)
It looks like you are trying to bond the Fe atom to a nitrogen that already
has a proton attached to it.
Developers (or anyone): it would be good to check how the heme parameters
in the contrib data base (which were made in the 1980's) work with current
force fields....the question is not in the parameters themselves (which
are not perfect, but which were fairly extensively optimized against
experimental data), but whether the extra atom types used don't conflict
with any new atom types that have been added for ff14SB (say).
....dac
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Received on Sat Jun 04 2016 - 21:30:03 PDT
