Dear All
I am doing the alanine screening method using MM-PBSA method as implemented in AMBER 9 to calculate the binding free energy for the association of two proteins.
In ADVANCED TUTORIALS TUTORIAL 3 (MM-PBSA) we have to perform a seperate MD simulation of the mutated form of structures; subsequently, binding free energy can be calculated for complex of two proteins.
In order to save time, I would like to obtain several snapshots of mutated form of structures from the wild-type trajectory by atomic coordinate removal and calculate the binding energy so in this way it is assumed there is no significant structural change upon mutation.
I performed the mutation and calculate the binding energy using the trajectory of wild type of complex of protein. It was observed that the values for calculated GBTOT and PBTOT were too high (for example 2526564) I think there is something wrong with this method,
I would be grateful if some one help me in this regard.
Best regards,
Maryam
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Received on Sat Jan 02 2010 - 01:00:03 PST
