On 14/11/2011, at 11:12 a.m., Ben Roberts wrote:
> 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.
Further to this email, here is the procedure used:
"I was modeling Nickel so I started with known zinc parameters. I created a grid of parmtops spaced out by small delta sigma and delta epsilon originating from the zinc parameters. Then I ran TI calculations for forming of a Ni2+ ion (plus two Cl- ions) in a TIP3P bath with PME electrostatics. I then compared the hydration free energies to what I should expect from experimental results. I just kept the ones that best matched experiment." -- Dan Sindhikara
More details can be found in this publication: http://pubs.acs.org/doi/abs/10.1021/bi9013352
Let me know if you have any questions. Good luck!
Cheers,
Ben
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Mon Nov 14 2011 - 16:00:04 PST
