I have made a protein-protein docking and performed simulations using Gromacs. I want to make a hydrogen bond study on it using gmx hbond. 1. The docked complexes residues are not in a continuous sequence. (eg. Chain A has 1 to 100 and Chain B has 1 to 90). 2. The atom numbers were sequentially arranged. (eg. Chain A has 1-2000 atoms and Chain B has 2001-4000 atoms) 3. So I have created two separate ndx files with chain A and chain B separately. Now how to proceed with hydrogen bond analysis between these two chains?
Hi,
Cat/combine the two ndx files together (make sure they have unique group names).
When you run the analysis, select the first group when prompted, and then the second group.
Assuming those are the only two groups, you can also do this:
echo 0 1 | gmx hbond
I agree with Mr. John H Dupuis. You can also make two groups for chain A and chain B based on atom numbers in the same index.ndx and then run the command,
gmx_mpi hbond -f complex.xtc -s md.tpr -num hbond.xvg -n index.ndx -tu ns
When the groups are prompted select the desired groups for which hbond has to be calculated.
In case, a more comprehensible analysis is required, contact analysis with MDcons is a way to go where we will get to know which residues in chain A forms interactions with which residues in chain B through the course of time.
Hi Dr Thirumal Kumar D ! I would even suggest you to calculate contact maps in different time intervals for proteins using VMD. It can give you an idea about which residues from what chains are associating most.
- Badges
- Science topic
- Similar topics
- Physical Sciences
- Atomic, Molecular and Optical Physics
- Atoms