Defining groups.

[ivandatasci]

Hello everyone.

Could I have some guidance to address a simple question?

I intend to compute the energy of binding in a heterotrimeric complex.
The three peptide chains are named H, L, and X.

My "protein" is the heterodimer of peptide chains H and L.
My ligand is peptide chain X.

How do I indicate that grouping?

I am attaching my .pdb in case it helps.

Thank you.

Ivan
complex.pdb.gz

[Valdes-Tresanco-MS]

In gmx make_ndx:

1. use splitch to split the (1) Protein group into chains. For example splitch 1. This will generate an additional 3 groups.
2. Using | select H and L. For example, 20 | 21. This will generate a new group.
3. Save and quit

Then use those groups in gmx_MMPBSA.
Note: Use the tpr file otherwise you can't split the chains. For example, gmx make_ndx -f md.tpr -n index.ndx