Dear all,
I am interested to run MD simulation to look closer into the mode of interactions between different ligands and protein. My target protein is a homotetramer and I have selected it's chain A for my study. In literarture, It is mentioned that It has an elongated active site, which is primarily formed by a A chain and some residues from C-terminus D chain are also located close to it. In that case, I am using both chains for running MD. My question is, can I use chain A complex with ligand while chain D without ligand to mimic original system? or I should use both chains in complex with ligands? Your help is appreciated.
(I am only interested to study chain A but due to elongated active site, I m also using D chain.)
By freezing of the unnecessary groups it is possible.
So you can run the MD simulation including a frozen part of your system.
It is needed to create an index file (.ndx) with the groups that you want to freeze.
Please Note that for each group defined as freezegroup you need to specify the dimensions that you want to freeze (x y z)
There are some other options for freezing too
Amber parameters are used for standard residues, and Amber's Antechamber module (included with Chimera) is used to assign parameters to nonstandard residues.
freeze none | selected | unselected | atom-spec
Which atoms (in addition to those frozen automatically) to hold in place during minimization: none (default), those which are selected, those which are not selected, or those indicated with an atom-spec.
Previously this option was required to freeze any atoms, but now that atoms other than the spec atoms are frozen automatically, this option is only needed in the case of:(1)restricting the calculation to certain residues with the spec option and fragment true (2)additionally freezing some of the spec atoms
spec atom-spec
Minimize/move only the atoms in atom-spec. All other atoms will be held in place automatically, without explicit use of freeze. However, energy calculations will include the entire molecule models containing the specified atoms, unless fragment true is also used. All included models are treated as a single system. If atom-spec contains any spaces, it must be enclosed in single or double quote marks.
Thank you sir for quick response. After reading your suggestion, I understand that I should restrain chain D except those residues which are close to chain A. Am I right?
Yes, It is one of the solutions, There are also other ways . If you want, we can discusses more about it or simulate it together
Dear Saman
You sent me the "4cm6" as your target pdb. id, but I can't find it
Please send me the input file of your target if it is available , then I will run some docking calculation for you
- Badges
- Science topic