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

[Pappu Kumar]

I have already used g_hbond. I am not sure how accurate is the H-bond lifetime calculation. Also the trajectory snapshots need to be saved quite often. Could you tell me how to interpret output from g_hbond -ac :

@ s0 legend "Ac\sfin sys\v{}\z{}(t)"
@ s1 legend "Ac(t)"
@ s2 legend "Cc\scontact,hb\v{}\z{}(t)"
@ s3 legend "-dAc\sfs\v{}\z{}/dt"

Could you tell me how to  project the configurations of the mutant simulation on WT PC1? Are you aware of any paper where I can read more about it? Can I compare the PC1 vs PC2 in case of WT and mutant?


I am trying to find out how such mutation buried inside the protein away from the ligand binding pocket can influence the function of the protein. I actually see some changes in the positon of the bound ATP in the mutant compared to the WT. But I am not sure how reliable it is due to the inaccuracies in parameterization. 


I also calculated the Gibbs free energy landscape by g_sham using Rg and RMSD. The value varies from 0-6.5 kJ/mol in both cases but the regions with ~0 kJ/mol has changed. 


Thank you.