Entry: NAFlex_BSC1-OL4


Nucleic Acid Data:


SequenceCGCGAATTCGCG
Rev. SequenceCGCGAATTCGCG
TypeDNA
SubTypeB
Chainsduplex
Pdb1NAJ [PDB] [NDB]
LigandsNo
KeywordsDNA-B Duplex Naked OL4 TIP3P Electroneutral


Simulation Metadata
Force FieldparmBSC1
Simulation Date2015-Aug-03
Simulated Time1,500 ns
Time Step1 ps
PartsDNA+ions
Temperature298K
WaterTIP3P
Additional SolventNo
Counter IonsNa+
Ionic ConcentrationElectroneutrality
Additional IonsNo
Additional MoleculesNo
Ions ParametersDang
Unified Molecular Modeling (UMM) Metadata
(Click to see full UMM)
Simulation Metadata (UMM)
AdditionalIonsNo
AdditionalMoleculesNo
AdditionalSolventNo
AuthorI.I.
Chainsduplex
CommentsFF Validation
CounterIonsNa+
Formatmdcrd
FrameStep1 ps
Frames1500000
IonicConcentrationElectroneutrality
IonsParametersDang
LigandsNo
NucTypeDNA
PDB1NAJ
PartsDNA+ions
RMSd_avg1.798
RMSd_stdev0.327
Rgyr_avg13.274
Rgyr_stdev0.265
SASA_avg4385.481
SASA_stdev71.449
SubTypeB
Temperature298K
Topologyno_wat.OL4.top
Trajectorynaked.OL4.5000.trj
WaterTIP3P
_idNAFlex_BSC1-OL4
altPDB101D 109D 127D 128D 129D 130D 144D 166D 170D 171D 1BNA 1D30 1D43 1D44 1D45 1D46 1D64 1D85 1D86 1DAU 1DNH 1DOU 1DPN 1DUF 1EDR 1EEL 1EHV 1EI4 1FMQ 1FMS 1FQ2 1FTD 1G3X 1GIP 1I3T 1I47 1JGR 1LEX 1LEY 1M6F 1N1O 1NAJ 1NGT 1PRP 1QV4 1QV8 1QXB 1VE8 1VZK 1ZPH 1ZPI 227D 233D 265D 266D 267D 268D 269D 270D 289D 290D 291D 298D 2B0K 2B3E 2BNA 2DAU 2DBE 2DYW 2GVR 2GYX 2I2I 2I5A 2L7D 2NLM 2QEG 2RF3 2RMQ 302D 303D 311D 328D 355D 360D 388D 389D 3BNA 3D0P 3OIE 3OPI 3U05 3U08 3U0U 3U2N 426D 428D 436D 442D 443D 444D 445D 447D 448D 449D 453D 455D 457D 460D 461D 463D 478D 4AGZ 4BNA 4C63 4C64 4DNB 4GJU 4GLG 4MKW 4OPJ 4QC7 4U8A 4U8B 4U8C 5BNA 6BNA 7BNA 8BNA 9BNA
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
datasetArray
date2015-Aug-03
descriptionDNA-B Duplex Naked OL4 TIP3P Electroneutral
forceFieldParmBSC0-OL4
ionsModel-
moleculeTypeDna
rev_sequenceCGCGAATTCGCG
saltConcentration-
sequenceCGCGAATTCGCG
soluteAtoms758
soluteCharge-22
soluteResidues24
solventAtoms-
solventResidues-
time1,500
totalAtoms758
totalCharge-22
totalIons-
totalResidues24
Quality Control
RMSd1.798 (0.327) Å    
Rgyr13.274 (0.265) Å    
SASA4385.481 (71.449) Ų    
RMSf