Hi Ben,
van der Waals parameters of the Manganese I have obtained by the
website
http://www.pharmacy.manchester.ac.uk/bryce/amber,I don't know how to
put these MN2+ parameters into metalparm.xml and metals.xml,how should I
solve this problem,and I will create manganese protein available by MCPB.
Best Regard
JiYuan
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
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Received on Thu Nov 17 2011 - 22:30:03 PST
