I have generated parameters for Doxorubicin using ATB server to be used with gromacs. I have calculated solvation free energy of doxorubicin (parameters generated by ATB) which gives a value around -2.02 KCal/mol using the "free energy of solvation" tutorial given at gromacs website( with lambdas instead of setting for vaderwaals, I have set different values for the fep-lambda term). The experimental value found in the literature is around 18.08KCal/mol. Am I doing the calculations somewhere wrong or can anybody please suggest any other method along with steps(as I am new to gromacs) to check the parameters.
Thanks
Theoretical methods do not necessarily reproduce the experimental results due to many factors, perhaps your theoretical protocol is not considering all the parameters considered in the experimental part. Maybe you can start to validate the computaional protocol by trying to reproduce a tutorial in which the theoretical procedure reproduces the experimental data and also consider the protonation state of your ligand and most of factors present in the experimental report.
So in my theoretical protocol ,should I do calculations with the values set for coulombic lambdas, bonded lambdas and restraint lambdas and then add the values from all these to get the solvation free energy?
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