Entry: NAFlex_1vt5


Nucleic Acid Data:


SequenceCCCCGGGG
Rev. SequenceCCCCGGGG
TypeDNA
SubTypeA
Chainsduplex
Pdb1VT5 [PDB] [NDB]
Ligandsno
KeywordsDNA-A Duplex Naked ParmBSC1 TIP3P Electroneutral


Simulation Metadata
Force FieldparmBSC1
Simulation Date2015-Apr-25
Simulated Time200 ns
Time Step1ps
Partsions + DNA
Temperature300K
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
AuthorA.P.
Chainsduplex
Comments/orozco/scratch/parmBSC1/Alberto2/1vt5
CounterIonsNa+
Formatmdcrd
FrameStep1ps
Frames200000
IonicConcentrationElectroneutrality
IonsParametersDang
Ligandsno
NucTypeDNA
PDB1VT5
Partsions + DNA
RMSd_avg2.712
RMSd_stdev0.457
Rgyr_avg10.277
Rgyr_stdev0.245
SASA_avg2968.466
SASA_stdev57.231
SubTypeA
Temperature300K
Topology1vt5.dry.top
Trajectory1vt5.trj
WaterTIP3P
_idNAFlex_1vt5
altPDB187D 1RXA 1RXB 1VT5 259D 2A0P
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-Apr-25
descriptionDNA-A Duplex Naked ParmBSC1 TIP3P Electroneutral
forceFieldparmBSC1
ionsModel-
moleculeTypeDna
rev_sequenceCCCCGGGG
saltConcentration-
sequenceCCCCGGGG
soluteAtoms502
soluteCharge-14
soluteResidues16
solventAtoms-
solventResidues-
time200
totalAtoms502
totalCharge-14
totalIons-
totalResidues16
Quality Control
RMSd-
Rgyr-
SASA-
RMSf-