RE: Phosphotyrosine Parameters/Toplogy

From: Lennart Nilsson (Lennart.Nilsson_at_ki.se)
Date: Fri Jan 25 2019 - 14:35:51 CST

Phosphotyrosine is already present since many years in the CHARMM36 force field as patch TP1 in:
toppar/stream/prot/toppar_all36_prot_na_combined.str

Get to know the files that you have to work with – much better than just asking somebody else to help you out (and asking a CHARMM FF question at the NAMD site may not always work out well)!
Also remember: grep and google are your friends!

Best wishes,
Lennart Nilsson

From: owner-namd-l_at_ks.uiuc.edu [mailto:owner-namd-l_at_ks.uiuc.edu] On Behalf Of Vermaas, Joshua
Sent: den 25 januari 2019 20:57
To: alexsaadfalcon_at_gmail.com; namd-l_at_ks.uiuc.edu
Subject: RE: namd-l: Phosphotyrosine Parameters/Toplogy

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<mailto: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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