Dear Marek,
>> I am just thinking about the possibility of calculating
>> free energy of solvation for the given molecule using MM/PBSA.
>>
>> Let say that I have (i) MD trajectory of the given molecule from
>> simulation in vacuum and
>> (ii) MD trajectory from simulation of the same molecule in explicit
>> water.
>>
>> If I am not wrong, enthalpic contribution to the complete solvation
>> energy
>> could be estimated like:
>>
>> H(solvated molecule) - H(molecule simulated in vacuum)
>>
>> ( where H(solvated molecule) contains also interaction energy with
>> solvent
>> )
why not just use pbsa (in sander?) or delphi as a standalone program? It
should give you the free energy of solvation for your molecule, maybe
based on some MD snapshots. Using MMPBSA for the analysis would just add
the change in internal FF-energy upon transferring the molecule to vacuum,
which would not be very accurate in any case.
Thomas
Dr. Thomas Steinbrecher
formerly at the
BioMaps Institute
Rutgers University
610 Taylor Rd.
Piscataway, NJ 08854
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Received on Wed Jun 15 2011 - 08:00:09 PDT
