Since I have MDs produced with GROMACS, are there available any tool for calculating dGs with MM/GBSA method? (and, in the meanwhile, without converting trajectories in AMBER format?)
In fact, there are accessory programs that do this. See, for instance, http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3471955/pdf/pone.0046902.pdf. The group that produced this paper makes the software freely available.
In fact, there are accessory programs that do this. See, for instance, http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3471955/pdf/pone.0046902.pdf. The group that produced this paper makes the software freely available.
The real problem in your case would be the force field you have used in gromacs MD engine. Converting the trajectory format from gromacs format to other formats available should not be a real problem. If you, for instance, have used amber force field, then you can use amber tools for MM-PBSA/GBSA calulations, just convert the trajectory to amber format.
Hi Dario,
please contact me if you want a new version of our gmxpbsa tool to calculate MM/PBSA under Gromacs.
Thank you Andrea,
actually we have just purchased a license for AMBER14. Nevertheless I will contact you soon.
Hi there,
we released a new version of GMXPBSA 2.1: http://www.sciencedirect.com/science/article/pii/S0010465514003154 and you can freely download the tool either from CPC library or http://gdriv.es/gmxpbsa where you can download the DEMO files too. Moreover, we set up a mailing list in case you need help with this tool: https://groups.google.com/forum/#!forum/gmxpbsa
hope it helps
Great! Actually I am focused on a docking work, therefore I am using MM-GBSA calculation implemented with the Schrodinger suite. Soon I will return on my MD project and then I will try your tool. Keep in touch...
There is a paper for a tool to do this with GROMACS.
g_mmpbsa—A GROMACS Tool for High-Throughput MM-PBSA Calculations
http://pubs.acs.org/doi/abs/10.1021/ci500020m
Also, you will find a tutorial for using it. It is straightforward and easy to follow.
http://rashmikumari.github.io/g_mmpbsa/
I hope you find them useful.
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