Hello Hassan,
Dr. Cheatham's parameters for heme, as Mark suggested, work great for me. But the problem you experienced appear to be another story, as LeaP unable to recognize the atom type given in the parameter files. If my memory serves, the Bryce Group parameter use different atom types as AMBER people usually do, e.g. they use atom type (not atom name) of NP (or ND?) which rarely used in AMBER force fields. That's probably the cause of your problem.
Try Mark's suggestion, if you still want to stick to Bryce's one, modify the atom type properly or use add 'missing' atom types accordingly using 'addatomtypes' command in LeaP.
Good luck,
Yue
On May 31, 2012, at 3:16 AM, Mark Williamson wrote:
> On 31/05/2012 01:48, hwchem chem wrote:
>> Dear Amber users,
>>
>> I would like to run MD simulation for cytochrome complex but I am facing a problem with the HEM force field.
>> As you know, Antechamber, can't be used for that because of the Fe atom.
>>
>> I found some articles about that such as,
>>
>> J. Phys. Chem. B 2008, 112, 8165–8173
>> Chem. Rev. 2004, 104, 3947-3980
>> J. Am. Chem. SOC1.9 93,115, 9620-9631
>> Also, I tried to use the force field found by Bryce Group, (heme-all-atom) http://www.pharmacy.manchester.ac.uk/bryce/amber
>>
>
> Dear Hassan,
>
> Have a look at the supporting information in
> http://dx.doi.org/10.1002/jcc.21922
>
> Regards,
>
> Mark
>
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Received on Thu May 31 2012 - 19:00:03 PDT
