Hi Yogesh,

Just take two proteins and follow the native protein MD simulation protocol.

You do not need to use any software or webserver to generate the topology.

Topology files of both protein will be generated by GROMACS only.

I have done the same as mentioned above for protein-protein MD in GROMACS.

This will help you definately.

If you face any problem, msg me.

@Dear Vikram Dala Please elaborate your answer. Your said to follow native gromacs steps, how gromacs will generate topology and by which command. Please suggest command or tutorial, it will be great help for me. Thank you in advance

Dear Yogesh,

Please go through these tutorials:-

http://www.mdtutorials.com/gmx/lysozyme/index.html

https://www.youtube.com/watch?v=rYZ1p5lXNyc

Both will help you alot.

I hope this will work for you.

Visit this website:

http://mdtutorials.com/gmx/ and find suitable tutorial as per your requirement.