[gmx-users] C-terminal amide capping

ANINDITA GAYEN aninditagayen at yahoo.co.in
Fri Feb 20 14:45:55 CET 2009

Dear all,

            I do
simulate DMPC+peptide+water+ions system, using OPLS-AA force field.

My peptide has N-terminus: NH3+ & C-terminus: COO- groups. I want to convert it to 

N-terminus: NH2, C-terminus: CONH2. The N-terminal capping is easily
done using "pdb2gmx -ter " command, but C-terminal amide capping option
is not incorporated.

Can anyone please suggests me how i can achive this?

Thanks in advance.

Ms. Anindita Gayen
C/O Dr. Chaitali Mukhopadhyay
Senior Research Fellow

Department of Chemistry

University of Calcutta

92, A. P. C. Road

Kolkata-700 009


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