In order to obtain the prmtopof the two domains, I guess you could "divide
the domain" with Pymol or VMD, and save two pdb, one for each domain. Then
with different pdb you can build two different prmtop.
I hope this works.
Bye
2010/7/19 Catein Catherine <askamber23.hotmail.com>
>
> Dear Sir/Madam,
>
>
>
> I am trying to calculate the interaction energy between domain 1 and 2 of a
> protein. Since domain 1 and 2 are connected, i cannot define a separated
> prmtop file for each domain. I guess I cannot use MMPBSA/GBSA methods to
> get this interaction energy. Are there any other methods I can use to
> estimate the binding energy between domains?
>
>
>
> Best regards,
>
>
>
> Cat with thanks.
>
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Received on Mon Jul 19 2010 - 01:00:04 PDT
