Hello AMBER users,
For one of my projects, I have to model cysteine sulfur and glycine carbonyl thioester bond. I looked at the PyRED served tutorial, and from my understanding, I have to cap NH2 and COO of CYS with conventional NME and ACE cap groups. I also have to cap cysteine S with COO-CH3 and GLY COO-with S-CH3 and remove them in my project config file with no Intra and Inter charge. The obtained mol2 files will then be taken to parmchk2 to obtain modified frcmod for both residues.
Is it correct? Any suggestions will be appreciated.
Thank you.
-Tejas.
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Received on Mon Nov 06 2023 - 09:00:02 PST
