ANINDITA GAYEN wrote:
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.
What do you mean, "not incorporated"? You should be able to do it exactly as
you did with the N-terminus. You must include the -NH2 in your structure file,
and then process with pdb2gmx -ter.
-Justin
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
India
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--
========================================
Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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