I have performed a protein-protein simulation. I wish to see the change in binding between protein chain A & chain B. How to create a index files of chain A & B and do the analysis?
Like GROUP 1 : Chain A & GROUP 2: Chain B
Chain identifiers are valid entries in make_ndx, so "chain A" and "chain B" can be used, if the input file (e.g. PDB) contains the chain identifiers. Otherwise, you have to specify the residue numbers that pertain to each chain.
For creating a single index file of two chains, "chain identifiers" in the *.pdb file is the best way.
Lakshmanan Loganathan how can chains be identified in .pdb file ? could you give an example here ? if i want to identify chains in my .pdb file then how can i perform this task ?
Many thanks
Hai Ayesha Kanwal , It is very simple, I have given an example below to identify the chain name.
The below data can be seen in every pdb structure file. The bolded letters describe the chain name. Just look the similar data in your pdb file.
ATOM 1 N GLY A 99 -22.323 -16.677 -15.703 1.00
ATOM 2 HN GLY A 99 -22.809 -15.947 -15.260 1.00
ATOM 3 CA GLY A 99 -20.953 -16.950 -15.327 1.00
ATOM 900 N GLY B 111 19.222 -30.610 7.804 1.00
ATOM 901 HN GLY B 111 18.922 -30.369 8.707 1.00
If you still have doubt send me the file, I will help you.
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