<html><head><style type="text/css"><!-- DIV {margin:0px;} --></style></head><body><div style="font-family:times new roman,new york,times,serif;font-size:12pt"><div>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. <br>Jianguo<br><br></div><div style="font-family: times new roman,new york,times,serif; font-size: 12pt;"><br><div style="font-family: times new roman,new york,times,serif; font-size: 12pt;"><font face="Tahoma" size="2"><hr size="1"><b><span style="font-weight: bold;">From:</span></b> anna Kalkbrenner <anna.kalkbrenner@gmail.com><br><b><span style="font-weight: bold;">To:</span></b> gmx-users@gromacs.org<br><b><span style="font-weight: bold;">Sent:</span></b> Sunday, 20 March 2011 11:59:34<br><b><span style="font-weight: bold;">Subject:</span></b> [gmx-users] C-terminal amidation of peptide<br></font><br><meta
http-equiv="x-dns-prefetch-control" content="off">Hello,<br><br>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?<br>
<br>Best regards,<br><br>Anna<br>
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