Trying to calculate a structure using sa.inp script and the energy in the cooling loop increases instead of going down.
In the end there is a message
****&&&& rerun job with smaller timestep (i.e., 0.003)But making the timestep smaller does not help. Could anyone suggest where to look?
edit: I've also commented out my restrains thinking that maybe my noe's are too whacky, but still structure diverges.
Thanks!
Check if somebody has answered this question on NMRWiki QA forum
Did you find this post helpful? |
Similar Threads
Thread
Thread Starter
Forum
Replies
Last Post
[NMR paper] Automated NMR structure calculation with CYANA.
Automated NMR structure calculation with CYANA.
Related Articles Automated NMR structure calculation with CYANA.
Methods Mol Biol. 2004;278:353-78
Authors: Güntert P
This chapter gives an introduction to automated nuclear magnetic resonance (NMR) structure calculation with the program CYANA. Given a sufficiently complete list of assigned chemical shifts and one or several lists of cross-peak positions and columns from two-, three-, or four-dimensional nuclear Overhauser effect spectroscopy (NOESY) spectra, the assignment of the NOESY...
nmrlearner
Journal club
0
11-24-2010 09:25 PM
[NMR paper] Protein structure calculation from NMR data.
Protein structure calculation from NMR data.
Related Articles Protein structure calculation from NMR data.
Methods Mol Biol. 2002;173:267-83
Authors: Mal TK, Bagby S, Ikura M
nmrlearner
Journal club
0
11-24-2010 08:49 PM
[Question from NMRWiki Q&A forum] How to set up RAMA database restraints for NIH-XPLOR (for peptide NMR structure calcu
How to set up RAMA database restraints for NIH-XPLOR (for peptide NMR structure calculation)?
Hello, has anyone managed to set up RAMA restraints for NIH-XPLOR? For some reason I'm always getting E(RAMA)=0.000 in the output, that is the term is registered, but the the energy is always zero.
Somehow either parameters for the interaction are assumed to be zero or there are no atoms that have those energy term... Thanks.
In my sa.inp I've got the following setup:
!(1) initial setupevaluate ($krama = 1.0) !intraresidue proteinevaluate ($kramalr = 0.15) !long range proteinevaluate...
nmrlearner
News from other NMR forums
0
11-02-2010 11:22 PM
Structure Calculation Using CS-DP ROSETTA from NESG Wiki
Structure Calculation Using CS-DP ROSETTA
This is a copy of instructions for CS-DP Rosetta from NESG Wiki that was created on 8/20/19. Please go to the original post at http://www.nmr2.buffalo.edu/nesg.wiki/Structure_Calculation_Using_CS-DP_ROSETTA
for a more up-to-date version.
Introduction
The CS-DP-Rosetta approach merges the ideas of model generation using CS-Rosetta with model filtering by agreement to NOESY data via the DP-score from the RPF program to generate high accuracy protein structures. This hybrid approach uses both local backbone chemical shift data...
markber
BioNMR Wiki
0
08-20-2010 12:22 PM
protein structure calculation
Hi! every one!
I wanted to get in contact with people solving the structure of protein by using NMR. I am learning the process and i have many basics problem related with the work.
cheers!
premprakash
NMR Questions and Answers
0
03-29-2007 02:33 PM
PASD: auto NOE assignment & structure calculation
Completely Automated, Highly Error-Tolerant Macromolecular Structure Determination from Multidimensional Nuclear Overhauser Enhancement Spectra and Chemical Shift Assignments
Kuszewski, J.; Schwieters, C. D.; Garrett, D. S.; Byrd, R. A.; Tjandra, N.; Clore, G. M.;
J. Am. Chem. Soc. 2004; 126(20); 6258-6273
http://pubs.acs.org/isubscribe/journals/jacsat/126/i20/figures/ja049786hn00001.gif
Abstract:
The major rate-limiting step in high-throughput NMR protein structure determination involves the calculation of a reliable initial fold, the elimination of incorrect nuclear Overhauser...
How to keep XPLOR structure calculation from exploding?
Linear Mode
