[gmx-users] The solvation free energy of small ligand in water

Tanping Li jia_11_osu at yahoo.com
Fri Feb 24 21:00:29 CET 2012

Dear gmx users,

I know this is a old topic. I searched the mailing list however haven't find a answer.

I am calculating the solvation free energy of a small ligand in water, using FEP theory. Two steps are applied: firstly decrease the atomic charge to zero; secondly decrease the VDW to zero. I am really confused by the first step now.

1) Does FEP work for the ligand with the net charge being zero, yet the atomic charge is not zero? Journal results show that the finite size effect, which mostly comes from self-potential correction, is necessary for the Ewald/PME.(Hummer, Pratt and Garcia V100, 1206, 1996) 
As far as my understanding, the self-potential correction is still there even for the ligand with net charge of zero. I don't know where I missed up here. 

2) Is there a way to calculate the solvation energy of a charged ligand, for example, whose net charge is 1 in Gromacs? The paper by Darden Pearlman and Pedersen, V109, 10921 shows that sander in amber seems has the option to include the self-potential term, thus obtain the free energy. Does the newest version of Gromacs supply the similar function?

I really appreciate your consideration and help on this. 

Best regards and have a good weekend

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