Starting at Xplor-NIH 2.26 (now it’s version 2.29 on Feb. 8th, 2012), official Xplor-NIH package provides an example script doing explicit solvent refinement. The short description made by Xplor-NIH author: ============ wrefine.py: refinement with explicit solvent and full electrostatics. Includes*rdcs, noes, jcoupling terms and dihedral restraints. This is a*work-in-progress. Please compare with other protocols. In*particular, [...]
[CNS Yahoo group] water refinement problem - broken structure
water refinement problem - broken structure
Dear all, I'm trying to perform water refinement for the very first time (new CNS user), on an NMR ensemble of CYANA calculated protein structures but the end
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nmrlearner
News from other NMR forums
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07-18-2011 09:41 AM
[KPWU blog] Install Xplor-NIH 2.26 on new iMac (10.6)
Install Xplor-NIH 2.26 on new iMac (10.6)
A short note for installation of xplor-nih 2.26 on iMac. Few months ago, I downloaded XPLOR-NIH 2.26 for Mac OS and installed it on my new iMac (core i3, 3.06 GHz). The default configuration script does not include “Intel Core i3″ *in the processor list (at xplor-nih-xxx/arch/getDarwinCPU). The solution to make the configuration is to http://stats.wordpress.com/b.gif?host=kpwu.wordpress.com&blog=76132&post=234&subd=kpwu&ref=&feed=1
Go to KPWU blog to read complete post.
nmrlearner
News from NMR blogs
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12-25-2010 04:09 AM
[CNS Yahoo group] cns1.2 vs Xplor-NIH2.26
cns1.2 vs Xplor-NIH2.26
Hi all, I would like to know which are the differences between cns1.2 and XPLOR-NIH2.26 for NMR structure calculations. thanks simona
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[Question from NMRWiki Q&A forum] How to keep XPLOR structure calculation from exploding?
How to keep XPLOR structure calculation from exploding?
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.
nmrlearner
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11-02-2010 11:22 PM
[Question from NMRWiki Q&A forum] How to convert Xplor distance restraint to Amber?
How to convert Xplor distance restraint to Amber?
HiI am wondering if anyone knows a way to convert Xplor distance_restraint files to Amber format (7 or 8 column).RegardsRaman
Check if somebody has answered this question on NMRWiki QA forum
nmrlearner
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09-25-2010 07:47 AM
CNS water refinement scripts from RECOORD website
CNS scripts for water refinement of NMR-derived protein structures are available on the RECOORD website.
Reference:
RECOORD: A recalculated coordinate database of 500+ proteins from the PDB using restraints from the BioMagResBank
Aart J. Nederveen 1, Jurgen F. Doreleijers 2, Wim Vranken 3, Zachary Miller 4, Chris A.E.M. Spronk 5, Sander B. Nabuurs 5, Peter Güntert 6, Miron Livny 4, John L. Markley 2, Michael Nilges 7, Eldon L. Ulrich 2, Robert Kaptein 1, Alexandre M.J.J. Bonvin 1 *
1Bijvoet Center for Biomolecular Research, Utrecht University, Utrecht, The Netherlands
2Center...
nmrlearner
NMR structure calculation
0
05-21-2005 07:45 PM
Refinement against order parameter with XPLOR
New 2.10 release of XPLOR-NIH can now do a refinement against order parameters. You can get an idea what this refinement can be used for from the this paper.
Info about new features of XPLOR-NIH 2.10 from XPLOR-NIH website: - new parameter/topology file naming convention: NMR protein refinement should now use topology file protein.top and parameter file protein.par.
- new command: tclXplor which calls xplor -tcl. Can be used as command interpreter
- new potential term OrderPot to enable refinement against order parameters.
- update to PrePot from Junji Iwahara
- CSAPot: 15N CSAs...
water refinement in Xplor-NIH
Linear Mode
