On Sun, Dec 15, 2024, 王宇轩 via AMBER wrote:
>
>I am a beginner in MD simulation, and now trying to simulate CYP450 enzymes
>with CPDI using Amber22.
>
>I have read and followed the parameters for HEM-CPDI and CYP from Shahrok
>et al, 2012 (https://doi.org/10.1002/jcc.21922).
>However, I'm not sure if it is the best practice for parametrizing CPDI and
>its attached cysteine(CYP or CYM)
I would say this is still the best source for cytochrome-c and similar
systems. Others are welcome to chime in here.
>Apart from this, I received some disturbing messages when I saved amber parameters of my protein complex in tleap using Shahrok's parameters,
>althongh no error reported:
>
>> (Residues lacking connect0/connect1
>> these don't have chain types marked:
>> res total affected
>> CARG 1
>> CYP 1
>> HEM 1
>> NASN 1
Above are just informative messages, not intended to be "disturbing". (I
would agree that this distinction is not easy for users to make.) In this
case, the "Residues lacking" section can be ignored if tleap runs to
completion without errors.
...good luck...dac
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Received on Mon Dec 16 2024 - 12:30:03 PST
