If you use CHARMM FF and Gromacs4.5 or later, you can use -ter in pdb2gmx and choose CT2 to add NH2 at C-terminus. For other FF, you may need to manually add NH2 in pdb file.
Jianguo ________________________________ From: anna Kalkbrenner <[email protected]> To: [email protected] Sent: Sunday, 20 March 2011 11:59:34 Subject: [gmx-users] C-terminal amidation of peptide Hello, I'm sorry if my questions are on the elementary level, as I am still learning how to use GROMACS. I would like perform an MD run on a peptide that has an amidated c-terminal. My understanding is that I can modify my PDB structure to include the NH2 group. Then, with pdb2gmx I use the "-ter" option and select "none" for the C-terminus. Is this correct? What is the best way to edit the PDB file to add the amide group? Can it be done through a structural editor? Best regards, Anna
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