I need to perform MD simulation, Does Desmond Academic/non- comercial tool by D.E shaw provides all the functions and modules fully to prepare protein and ligand? If anyone knows please forward response. Response will be appreciated.
Thank you
Yes, it can be done, but the main point worth noting is that, it works only in Linux machines and not windows. So, you have to install it on the Linux os.
And as Uttam suggested, we can't run protein preperation for adding missing side chains and residues to the protein in free version.
hope it helps before diving into the MD.
regards
Tanuj
@Mr.Utam pal sir and Mr.Tanuj Sharma sir, Thanks for your concerns
But I need to know that How can we do completion of incomplete protein structure (missing side chains, missing loops),which cannot be fixed for free and pH dependent protonation states which also cannot be generated for free either except for pH 7. So please suggest a way to complete these steps So that I can perform MD for my complexes.
Thank you
With best regards
Shah Altaf
For fixing missing side chains, missing loops, missing residues, its best to use some modelling program including Modeller, SwissModel, iTASSER or any other software.
pH problem cannot be overcomed in free version, as there is need to change the hydroxyl and hydronium ion concentrations in solvent. It is actually much easy to maneuver these features in AMBER and gromacs.
If you are planning to study some particular enzyme inhibition at a particular acidic and basic environment, then only there is need to perform pH specific MD studies. Otherwise, you can do MD studies in DESMOND at pH 7.
regards
Tanuj
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