Is there anyone who can explain how to lead hydrogens relaxation in AMBER? Is there any key words or..?

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Yoshinobu Ishikawa

Hi Maria,

Did you go through the tutorials of AMBER?

http://ambermd.org/tutorials/

Sk. Abdul Amin

I found these links (attached herewith) are very interesting and helpful.

1. http://ambermd.org/tutorials/advanced/tutorial25/section1.htm

2. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2750878/

You may follow these links.

Thanks.

Regards,

Jadavpur University, India.

Martin Klvana

# SHAKE bond length constraints...

ntc=1 # SHAKE is not performed (default)

ntc=2 # bonds involving hydrogen are constrained