In GROMACS, for calculation of inter-peptide hydrogen bonds, on choosing 'Protein' option twice from the index file (after the gmx hbond command) would give both intra- and inter- peptide hydrogen bonds.
If I have 'n' number of peptides in my species , to get inter-peptide hydrogen bonds , how should I specify the index groups?
Should it be like specifying each peptide in a separate group and then group the other peptides (n-1) in another group and calculate hydrogen bonds? Repeat the procedure for all and average ?
Is this method correct? Or there's a better alternative?
Hi Apramita,
You can create different groups with gmx make by selecting the residues of each peptide. For example, if you peptides are built by 20 residues and you have 5 peptides in your simulation box, in your topology file the second peptide would start from the number 21. Therefore, you can create the first group from residue 1 to 20 and the second from 21 to 40 and so on.
gmx make_ndx -f file.gro ... > r 1-20 > name 18 > r 21-40 > name 19 > q
Dear Martiniano,
Thank you for your answer. Once I specify the index groups as you said, I can calculate the individual hydrogen bonds between each pair of proteins.
So should I take the average of all such hydrogen bonds to be the average inter-peptide hydrogen bond number?
Hi Apramita,
Yes, as long as this value is determined by a statistical analysis of different simulations. Additionally, I would recommend that you obtain the representative structures of your complexes through a cluster analysis to compare your average hydrogen bond values with those that can be visualized in the 3D complex.
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