Respected Rose,
I did simple MMGBSA calculations of the output of the QM/MM run,
but the results were almost same as the simple MD run. The binding
energies in both calculations(simple MD run & QM/MM run) were almost
same. How can i consider QM/MM calculations as more approximate if it
gives same binding energy as simple MD run?
Kindly give me fundamental reason for this similarity.
Regards
Kshatresh
On 3/14/10, Ross Walker <ross.rosswalker.co.uk> wrote:
>> There is currently no working version of QM/MMGBSA to calculate the
>> binding
>> free energy in AMBER, although efforts are currently underway to
>> include
>> this implementation. A way for you to get around this would be to setup
>> the
>> unsolvated complex, receptor, and ligand mdcrds yourself, and then run
>> a
>> QM/MM using sander and set imin=5 to do a post-processing analysis on
>> all
>> three of those trajectories. You can grep out the energies and do the
>> statistics analysis yourself, also.
>
> What do you believe is the problem with using QM/MMGBSA? The QM/MM model in
> AMBER supports Generalized Born it should be a simple matter to do MMGBSA
> with it. Will the results be good? I have no idea but it should work right
> now. You might have to hack the perl scripts a bit but that shouldn't be too
> hard.
>
> If you know of more fundamental reasons why it wouldn't work I'd be happy to
> hear them and take a look.
>
> All the best
> Ross
>
>
> /\
> \/
> |\oss Walker
>
> | Assistant Research Professor |
> | San Diego Supercomputer Center |
> | Tel: +1 858 822 0854 | EMail:- ross.rosswalker.co.uk |
> | http://www.rosswalker.co.uk | http://www.wmd-lab.org/ |
>
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Received on Sun Mar 14 2010 - 12:00:02 PDT
