CNS Yahoo group Atoms distance in a molecular dynamics

		BioNMR > NMR community > News from other NMR forums
[CNS Yahoo group] Atoms distance in a molecular dynamics

Webservers

NMR processing:

MDD

NMR assignment:

Backbone:

Side-chains:

NOEs:

Structure from NMR restraints:

Ab initio:

Fragment-based:

Rosetta-NMR (Robetta)

Template-based:

GeNMR

I-TASSER

Refinement:

Amber

Structure from chemical shifts:

Fragment-based:

Homology-based:

Torsion angles from chemical shifts:

Preditor

TALOS

Promega- Proline

Secondary structure from chemical shifts:

CSI (via RCI server)

TALOS

MICS caps, β-turns

d2D

PECAN

Flexibility from chemical shifts:

RCI

Interactions from chemical shifts:

HADDOCK

Chemical shifts re-referencing:

NMR model quality:

NOEs, other restraints:

Chemical shifts:

RDCs:

Pseudocontact shifts:

Protein geomtery:

SAVES2 or SAVES4

Quality Control Check

NMR spectrum prediction:

FANDAS

MestReS

V-NMR

Flexibility from structure:

Backbone S2

Methyl S2

B-factor

Molecular dynamics:

Gromacs

Amber

Antechamber

Chemical shifts prediction:

From structure:

Shiftx2

Sparta+

Camshift

CH3shift- Methyl

ArShift- Aromatic

ShiftS

Proshift

PPM

CheShift-2- Cα

From sequence:

Shifty

Camcoil

Poulsen_rc_CS

Disordered proteins:

MAXOCC

Format conversion & validation:

CCPN

From NMR-STAR 3.1

Validate NMR-STAR 3.1

NMR sample preparation:

Protein disorder:

DisMeta

Protein solubility:

Isotope labeling:

Solid-state NMR:

Thread Tools

Search this Thread

Rate Thread

Display Modes

05-16-2012, 08:34 PM

nmrlearner

Senior Member

Join Date: Jan 2005

Posts: 23,780

Points: 193,617, Level: 100

Level up: 0%, 0 Points needed

Activity: 50.7%

Last Achievements

Award-Showcase

NMR Credits: 0

NMR Points: 193,617

Downloads: 0

Uploads: 0

Atoms distance in a molecular dynamics

Atoms distance in a molecular dynamics

Hello, I'm new on CNS. I would like to generate N structures during a molecular dynamics. I employed model_anneal.inp downloaded on

More...

Did you find this post helpful?

Similar Threads
Thread	Thread Starter	Forum	Replies	Last Post
[CNS Yahoo group] Re: Atoms distance in a molecular dynamics Re: Atoms distance in a molecular dynamics ... if you didn't touch traj_freq, it should... post the log-file, there might be a clue there. -- Oh, suddenly throwing a giraffe into a volcano to make water More...	nmrlearner	News from other NMR forums	0	05-16-2012 08:34 PM
[NMR tweet] http://www.book-lib.com/methods-in-molecular-biophysics-structure-dynamics-function.html #nuclear #magnetic #resonance #molecular Method http://www.book-lib.com/methods-in-molecular-biophysics-structure-dynamics-function.html #nuclear #magnetic #resonance #molecular Method Published by booklib2011 (Books For Your Life) on 2011-04-12T07:02:21Z Source: Twitter	nmrlearner	Twitter NMR	0	04-12-2011 07:13 AM
Impact of (15)N R(2)/R(1) Relaxation Restraints on Molecular Size, Shape, and Bond Vector Orientation for NMR Protein Structure Determination with Sparse Distance Restraints. Impact of (15)N R(2)/R(1) Relaxation Restraints on Molecular Size, Shape, and Bond Vector Orientation for NMR Protein Structure Determination with Sparse Distance Restraints. Impact of (15)N R(2)/R(1) Relaxation Restraints on Molecular Size, Shape, and Bond Vector Orientation for NMR Protein Structure Determination with Sparse Distance Restraints. J Am Chem Soc. 2011 Apr 4; Authors: Ryabov Y, Schwieters CD, Clore GM (15)N R(2)/R(1) relaxation data contain information on molecular shape and size as well as on bond vector orientations relative to...	nmrlearner	Journal club	0	04-06-2011 10:54 AM
Impact of 15N R2/R1 Relaxation Restraints on Molecular Size, Shape, and Bond Vector Orientation for NMR Protein Structure Determination with Sparse Distance Restraints Impact of 15N R2/R1 Relaxation Restraints on Molecular Size, Shape, and Bond Vector Orientation for NMR Protein Structure Determination with Sparse Distance Restraints Yaroslav Ryabov, Charles D. Schwieters and G. Marius Clore http://pubs.acs.org/appl/literatum/publisher/achs/journals/content/jacsat/0/jacsat.ahead-of-print/ja201020c/aop/images/medium/ja-2011-01020c_0002.gif Journal of the American Chemical Society DOI: 10.1021/ja201020c http://feeds.feedburner.com/~ff/acs/jacsat?d=yIl2AUoC8zA http://feeds.feedburner.com/~r/acs/jacsat/~4/3J1IyCLkQMQ	nmrlearner	Journal club	0	04-05-2011 10:37 AM
A topical issue: NMR investigations of molecular dynamics A topical issue: NMR investigations of molecular dynamics A topical issue: NMR investigations of molecular dynamics Content Type Journal Article Pages 1-4 DOI 10.1007/s10858-009-9345-8 Authors	nmrlearner	Journal club	0	01-09-2011 12:46 PM
Alanine Methyl Groups as NMR Probes of Molecular Structure and Dynamics in High-Molecular-Weight Proteins Alanine Methyl Groups as NMR Probes of Molecular Structure and Dynamics in High-Molecular-Weight Proteins Raquel Godoy-Ruiz, Chenyun Guo and Vitali Tugarinov http://pubs.acs.org/appl/literatum/publisher/achs/journals/content/jacsat/0/jacsat.ahead-of-print/ja1083656/aop/images/medium/ja-2010-083656_0009.gif Journal of the American Chemical Society DOI: 10.1021/ja1083656 http://feeds.feedburner.com/~ff/acs/jacsat?d=yIl2AUoC8zA http://feeds.feedburner.com/~r/acs/jacsat/~4/hxZ4cabF688	nmrlearner	Journal club	0	12-08-2010 10:04 AM
[NMR paper] NMR and molecular dynamics studies of the interaction of melatonin with calmodulin. NMR and molecular dynamics studies of the interaction of melatonin with calmodulin. Related Articles NMR and molecular dynamics studies of the interaction of melatonin with calmodulin. Protein Sci. 2004 Nov;13(11):2925-38 Authors: Turjanski AG, Estrin DA, Rosenstein RE, McCormick JE, Martin SR, Pastore A, Biekofsky RR, Martorana V Pineal hormone melatonin (N-acetyl-5-methoxytryptamine) is thought to modulate the calcium/calmodulin signaling pathway either by changing intracellular Ca(2+) concentration via activation of its G-protein-coupled...	nmrlearner	Journal club	0	11-24-2010 10:03 PM
[NMR paper] Conformation of parathyroid hormone antagonists by CD, NMR, and molecular dynamics si Conformation of parathyroid hormone antagonists by CD, NMR, and molecular dynamics simulations. Related Articles Conformation of parathyroid hormone antagonists by CD, NMR, and molecular dynamics simulations. Biopolymers. 1995 Oct;36(4):485-95 Authors: Chorev M, Behar V, Yang Q, Rosenblatt M, Mammi S, Maretto S, Pellegrini M, Peggion E The conformation of two highly potent parathyroid hormone (PTH) antagonists was investigated in water/2,2,2-trifluoroethanol mixtures. The two peptides are derived from the sequence (7-34) of PTH and of...	nmrlearner	Journal club	0	08-22-2010 03:50 AM

« Previous Thread | Next Thread »

Posting Rules
You may not post new threads You may not post replies You may not post attachments You may not edit your posts BB code is On Smilies are On [IMG] code is On HTML code is On Trackbacks are Off Pingbacks are Off Refbacks are Off