Hi,
MCPB.py could deal with HEME system. Here is a tutorial about MCPB.py: http://ambermd.org/tutorials/advanced/tutorial20/mcpbpy.htm <http://ambermd.org/tutorials/advanced/tutorial20/mcpbpy.htm>. When dealing with HEME system, you can treat the central Fe ion as a single residue, and the rest of the HEME group as another in the preparation PDB file.
Kind regards,
Pengfei
> On Jun 6, 2016, at 9:52 AM, Lachele Foley <lf.list.gmail.com> wrote:
>
> 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 Tue Jun 07 2016 - 20:00:03 PDT
