Re: [gmx-users] MM-GB/SA analysis in Gromacs

2013-02-01 Thread Ankita naithani
Hi Andrea, Thank you so much for bringing forth the paper. I have performed a MD simulation and would very much like to use the tool mentioned in the paper to calculate the binding free energy. Is it possible for you to kindly give me an access to the same and also a brief explanation as to how to

Re: [gmx-users] MM-GB/SA analysis in Gromacs

2012-11-29 Thread andrea spitaleri
Dear all, I would like to bring to your attention this paper http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0046902 in which we made a tool to perform MM/PBSA binding free energy calculation in automatic fashion, using torque/pbs parallel system implemented in most clusters

[gmx-users] MM-GB/SA analysis in Gromacs

2012-11-29 Thread Anna Marabotti
Dear gmx-users, I ran several MD simulations using Gromacs 4.5.4 version, and now I'd need to calculate binding free energies using the MM-GBSA method. I searched through the manual and through the gmx-users archive, but I didn't find a way to do it. I found an old post in which it appeared t