My title is not the exact description for my problem.
I was asked to calculate the free energy change of cation (Na+, K+) with acid group (COO-) on a protein using QM/MM method.
I used MD simulation all the time. I know it's easy to use thermodynamics integration to calculate the hydrogen dissociation on acid group. But I have no clue how to deal with cation and use QM/MM methods.
Does anyone give me some suggestion?
Thanks,
Xiaoquan.
Dear Xiaoquan,
I would suggest using CHARMM, please cf. the following URL address:
http://www.esi.umontreal.ca/accelrys/life/insight2000.1/charmm_principles/Ch06_free_energy.FM5.html
Respectfully yours,
Evgeni
Hi !
I just propose an alternative : CP2K
With a nice tutorial on what you want Lecture 13 in the following link
http://www.cp2k.org/exercises:2014_ethz_mmm:index
P.
Mr. Sun,
I do not know which software you use, but with Gaussian for example you can easy perform computation of ionic species such as the shown pairs for example COO-/Na+. Please find as attachment a simple computation of this pair using MM (UFF for example) thermochemistry along with the output parameters. There are other MM methods too. Separately are shown MD data.
More about Gaussian you can read at the following web-page: http://www.gaussian.com/
AMBER offers QM/MM thermodynamic integration by various routes. One trick is to integrate from QM to classical representation of a bound and restrained state (eg using the lambda parameter of SEBOMD), then phase out the restraints and the ion with normal classical TI, then integrate back to the QM model sans ion. That way the costly part of your calculation can still be done on a classical system.
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