There is a atom types table here:
http://ambermd.org/doc/AtomTypesTableWorkspace.xhtml
Let us know if it needs updating in some way.
On Sun, Jun 5, 2016 at 12:26 AM, David A Case <david.case.rutgers.edu> wrote:
> 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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--
:-) Lachele
Lachele Foley
CCRC/UGA
Athens, GA USA
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Received on Mon Jun 06 2016 - 07:00:03 PDT
