[gmx-users] Effect of a single mutation in a protein

Pappu Kumar papuu_k at yahoo.com
Wed Mar 26 16:00:06 CET 2014

I did 50 ns MD simulation of WT and mutant protein in gromacs with 
Amber ff99sb. The mutation alters the function of the protein. The RMSD 
and RMSF differences in WT and mutant are <1 A. I also calculated the change in entropy of the water molecules around 4 A by 
Schilter's formula which seems to change in case of the mutation. Let me know how to 
calculate the H-bonding lifetime of the water during the simulation. 
Further I plotted the PC1 of C-alpha atoms of WT with the PC1 of the 
mutant. I am wondering if it makes sense to compare PC1 from different 
trajectories. Please suggest me some possible analysis. Thank you. 

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