I would like to minimize the complex in AMBER before launching molecular dynamics and also to relax hydrogens prior to MD but can't find any keywords or anything about it..
Hi Maria,
Did you go through the tutorials of AMBER?
http://ambermd.org/tutorials/
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,
Sk. Abdul Amin
Jadavpur University, India.
# SHAKE bond length constraints...
ntc=1 # SHAKE is not performed (default)
ntc=2 # bonds involving hydrogen are constrained
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