I have modified the 'N' terminal ASP residue of a polypeptide. To make
parameter files of this modified AA, I have followed the following
steps-
1) Picked the modified AA part from the optimized structure of the
whole modified protein
2) Generated .ac file for the modified AA unit (link of the followed
protocol is mentioned below) using Antechamber
But the in output PDB file, side-chain carboxylate group of ASP made a
five-membered ring with C-terminal carbon of ASP residue when I gave
net charge zero in Antechamber. While I gave net charge as -1 and
multiplicity 3, the program did not run giving "fatal error".
Please suggest me how to tackle the terminal C atom and total charge,
also the procedure, that can be followed to generate parameter files.
http://ambermd.org/tutorials/basic/tutorial5/
Thanks,
Shankha Banerjee
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Received on Thu Sep 05 2019 - 11:30:02 PDT
