We did the Gromacs MD simulation for the protein complex , the complex is stable during 15 ns Simulation. We would like to plot the interface area plot for the protein complex along the entire trajectory (15ns) - how to do this or can we use any other Gromacs tools to show that the interface is stable during the simulation ?
Thanking you in advance
Hi, you may want use g_sas for this. Protein A and B in complex then you calculate SAS(A), SAS(B) and SAS(AB). Your interface will be:
Interface = A + B - AB
which is called buried surface area too.
hope it helps
andrea
Dear Mr. Penumutchu
an useful (and free) software to do this could be SURFINMD. The author (Mr. Diego Enry) can be contacted through e-mail (or ResearchGate) and you could request him the program. Follow the link: http://lmdm.biof.ufrj.br/software.html
Hi, you may want use g_sas for this. Protein A and B in complex then you calculate SAS(A), SAS(B) and SAS(AB). Your interface will be:
Interface = A + B - AB
which is called buried surface area too.
hope it helps
andrea
hi,can you teach me how did you run the protein-protein complex run by using GROMACS?
Hi,
I think that you can start by looking one of the tutorial here:
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/
and
http://www.gromacs.org/Documentation/Tutorials
Hi，i have learnt thetutorial，but there is nothing about how to do protein-protein complex,and i am not sure how to prepare the topol file~
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