I have generated a complex of antigen and antibody using haddock and used that cluster for MD run using Gromacs. Now I need to find out the inter hydrogen bonds formed between antigen and antibody complex. what commands do I need to give ?
you can use "gmx hbond -f md.xtc -s md.tpr -num hbond.xvg" and then select the two groups which you want to investigate the hydrogen bond between them.
This Antigen + antibody complex is a protein complex so when I am using command line gmx hbond -f md_0_50.xtc -s md_0_50.tpr -num hbnum_Pro-Pro.xvg -hx hbhelix.xvg.