[AMBER] the best APS is not zero, bonds involved by this atom are frozen

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From: Ashutosh Shandilya <izerokelvin.gmail.com>
Date: Mon, 6 May 2013 20:45:43 +0530

Dear Users
I have a modified peptide of three residue when I generate 3d coordinates
from different softwares they are different. Both the structures are quite
different from one another. I did minimization using sander it gave some
output but with other structure it gives error saying "*the best APS is not
zero, bonds involved by this atom are frozen"*. so I cant compare them.
Attached are the pdb files with two different softwares.

One more question how to define which one of them is the right structure?

Thanks
Ashutosh

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chemical/x-pdb attachment: B1.PDB

chemical/x-pdb attachment: newb1.pdb

Received on Mon May 06 2013 - 08:30:04 PDT