From: Vermaas, Joshua (Joshua.Vermaas_at_nrel.gov)
Date: Fri Jan 25 2019 - 13:57:26 CST
Do you mean parameterizing a new force field specific for PTR, or setting up a QM/MM simulation with PTR in the QM region? To get a new force field, CGenFF or FFTK would be my tools of choice. See https://www.ks.uiuc.edu/Training/Tutorials/science/forcefield-tutorial/forcefield.pdf for an overview, and ignore all the talk about SPARTAN. If you want QM/MM with PTR in the QM region, I don't think you even need to add bonds, although others would know more.
-Josh
On 2019-01-25 11:14:08-07:00 owner-namd-l_at_ks.uiuc.edu wrote:
What is the proper way to create a new residue for PTR (phosphotyrosine) as seen in the 2HDX pdb? It is easy enough to simply add bonds, but is there a way to run QM on just the new residue?
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