Entry: NAFlex_psATT


Nucleic Sequence:


Sequence 1:AAAAAAAAAA
Sequence 2:TTTTTTTTTT
Sequence 3:TTTTTTTTTT
Sequence 4:TTTTTTTTTT
TypeDNA
SubTypeparallel triplex ATT
Chainstriplex
Pdb-
Ligandsno


Force FieldparmBSC1
Simulated Time440 ns
Time Step1ps
Partsions + DNA
Temperature300K
Water ModelTIP3P
Additional SolventNo
Counter IonsNa+
Ionic ConcentrationElectroneutrality
Additional IonsNo
Additional Moleculesno
Ions ParametersDang
RMSd2.026 (0.243) Å    
RMSf
Unified Molecular Modeling (UMM) Metadata
(Click to see full UMM)
AdditionalIonsNo
AdditionalMoleculesno
AdditionalSolventNo
AuthorA.P.
Chainstriplex
Comments/orozco/scratch/parmBSC1/Alberto2/psatt10
CounterIonsNa+
Formatmdcrd
FrameStep1ps
Frames440000
IonicConcentrationElectroneutrality
IonsParametersDang
Ligandsno
NucTypeDNA
PDBno
Partsions + DNA
RMSd_avg2.026
RMSd_stdev0.243
Rgyr_avg12.547
Rgyr_stdev0.301
SASA_avg4945.904
SASA_stdev100.755
SubTypeparallel triplex ATT
Temperature300K
Topologypsatt10.dry.top
Trajectorypsatt10.trj.gz
WaterTIP3P
_idNAFlex_psATT
authorsIvan Ivani, Pablo D. Dans, Agnès Noy, Alberto Pérez, Ignacio Faustino, Adam Hospital, Jürgen Walther, Pau Andrio, Ramon Goñi, Alexandra Balaceanu, Guillem Portella, Federica Battistini, Josep Lluís Gelpí, Carlos González, Michele Vendruscolo, Charles A. Laughton, Sarah A. Harris, David A. Case and Modesto Orozco
boxAngle109.471219
boxX62.8063753
boxY62.8063753
boxZ62.8063753
datasetArray
date0.00000000 1430265600
descriptionDNA Triplex Naked ParmBSC1 TIP3P Electroneutral
forceFieldparmBSC1
ionsModel-
moleculeTypeDna
rev-sequence-
rev_sequenceTTTTTTTTTT
saltConcentration-
sequenceAAAAAAAAAA | TTTTTTTTTT | TTTTTTTTTT | TTTTTTTTTT
sequenceMultiArray
soluteAtoms957
soluteCharge-27
soluteResidues30
solventAtoms-
solventResidues-
time440
totalAtoms957
totalCharge-27
totalIons-
totalResidues30


Selection:
MDAnalysis Atom Selection Syntax
e.g. resid 2:11 or resid 13:20
Frame (start:stop:step)
Download

Format:        

Analysis

Analyse the selected trajectory using NAFlex server.