Re: protocol to start MD

From: Vlad Cojocaru (
Date: Wed Aug 19 2009 - 10:22:37 CDT

Well, your protocol is a bit strange ...
What about this one (of course the steps below refer to explicit water
simulations ... you always have the choice to do implicit solvent
simulations if you wish so)
1. obtain the 3-D of protein (from pdb)
2. check the quality of the pdb structure, check if complete ... if not
you'll have to see what to do with the missing parts ...
3. add hydrogens, check protonation states of buried amino-acids
4. neutralize and/or add salt
5. solvate
6. minimize with positional restraints on the experimentally determined
structure (this usually means all the atoms that were present in your
original crystal structure file)
7. gradually decrease the force constant for the positional restraints
8. heating shortly NVT (sau direct NPT) with positional restraints on
the experimentally determined structure
9. equilibrate NPT without positional restraints until reach proper
density and structural equilibrium (no jumps in rmsd and other
structural properties)
10. production runs in NVE, NVT sau NPT ...

Why do you want to clean protein from ligand and water ? You have to
have good reasons for this ...
Minimization in vacuo is also not really what you want ....

Hope this helps

jose correa wrote:
> Dear all
> I want to ask you about the protocol to star MD step by step:
> 1.- obtain the 3-D of protein (from pdb ect)
> 2.- clean it from water, ligands etc.
> 3.- minimization in vacuo
> 4.- solvate and ionize
> 5.- minimized water and ions freezing the protein
> 5.- MD of water and ions freezing the protein
> 6.- minimizing the whole system
> 7.- heating (MD) from 10 to 310 K
> 8.- Run a short MD under NTP
> 9.- Run the MD (large) under NTV
> Is it ok?, could you suggest me any reference?.
> Best wishes
> Josť Correa-Basurto
> ESM-IPN, mexico

Dr. Vlad Cojocaru
EML Research gGmbH
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