anna Kalkbrenner wrote:
Hello,
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?
Your approach is correct. Use your favorite editing software to add the
appropriate group. There are some useful programs listed on the Gromacs site,
but unfortunately it is currently down. xLeap is a pretty useful tool, although
there are many others that can accomplish the same; for simple amide addition
you could probably add it manually with a bit of geometry :)
-Justin
Best regards,
Anna
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
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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