Dear Amber professionals,
I am a new user of Amber. I met two problems when using Amber 10 sander for protein annealing (0K-1200K-0K) with some distance and angle constraints.
(1) I often met following problem:
"Coordinate resetting (SHAKE) cannot be accomplished, deviation is too large
NITER, NIT, LL, I and J are : XXXXXXXXXXXXXX
Note: This is usually a symptom of some deeper problem with the energetics of the system."
I sometimes can solve this problem by dividing the annealing input file(the file describing the steps and temperatures) to several files and run them one by one, but sometimes this problem remained. May I know the major causes and solutions for this problem?
(2) I got some cis-peptides when I use annealing-minimization to refine my protein structures. I know one solution is to put the omega=180 constrains to the peptide bonds for annealing. May I know whether there are another solutions? Or are there any programs can fix the geometry problems of a protein structures?
I look forward to your replies. Thank you very much.
Best regards,
Yiyu
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Received on Sat Jun 19 2010 - 20:30:03 PDT
