Hi Ji-Yuan,
On 14/11/2011, at 12:47 a.m., Áõ¼ªÔª wrote:
> I want to build my manganese protein by MCPB program,after I runed sh genMetalFF.sh -n 1AMP_OH,I looked for the settings file,I found that the file metals.xml and metalparm.xml does not include the mananese information,could I execute the next procedure,and I can get the MM parameters for my manganese protein?
I apologise for the delay in my response. The lack of metal parameters is a known problem in MCPB at the moment. As you have guessed, you'll need to add the appropriate parameters to the files metalParm.xml and metals.xml. You may find this process is not trivial (hence why only a few metals have been parameterised so far).
A former colleague of mine at one point used a thermodynamic integration (TI) method to obtain van der Waals parameters (the chief missing piece) for Ni2+ ions. I'll see if I can dig out the details of the procedure he used.
Regards,
Ben
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Received on Mon Nov 14 2011 - 08:30:03 PST
