On Thu, Jun 15, 2017, Saikat Pal wrote:
> Thank you sir for your kind response . This is my main pdb
> (2rd6-new.pdb) and after capping pdb (2rd6-leap-1.pdb).I have attached
> these pdbsin this mail.Thanks and regards,saikat
Your 2rd6-leap-1.pdb file is quite odd. It has two chains: the first chain
just has a single lysine residue. A single amino-acid peptide is non-standard
for Amber, since otherwise it doesn't know whether to treat the residue
as a N-terminal or C-terminal residue.
Of equal or greater concern, the position of LYS 1 is almost the same
as LYS 3. I don't really understand how you came up with this model, but
something seems to have gone quite awry. What happens if you just remove
LYS 1?
....dac
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Received on Thu Jun 15 2017 - 07:30:02 PDT
