Entry: NAFlex_2dgc


Nucleic Acid Data:


SequenceGGAGATGACGTCATCTCC
Rev. SequenceGGAGATGACGTCATCTCC
TypeDNA
SubTypeB
Chainsduplex
Pdb2DGC [PDB] [NDB]
LigandsNo
KeywordsDNA-B Duplex Complex ParmBSC1 SPC/E AddedSalt Protein-nuc


Simulation Metadata
Force FieldparmBSC1
Simulation Date2015-Apr-24
Simulated Time1,000 ns
Time Step1 ps
PartsDNA+protein+ions
Temperature298K
WaterSPCE
Additional SolventNo
Counter IonsK+Cl-
Ionic Concentration0.15M
Additional IonsNo
Additional MoleculesNo
Ions ParametersDang
Unified Molecular Modeling (UMM) Metadata
(Click to see full UMM)
Simulation Metadata (UMM)
AdditionalIonsNo
AdditionalMoleculesNo
AdditionalSolventNo
AuthorF.B.
Chainsduplex
Comments-
CounterIonsK+Cl-
Formatnetcdf
FrameStep1 ps
Frames1000000
IonicConcentration0.15M
IonsParametersDang
LigandsNo
NucTypeDNA
PDB2DGC
PartsDNA+protein+ions
RMSd_avg1.981
RMSd_stdev0.309
Rgyr_avg17.838
Rgyr_stdev0.322
SASA_avg6462.856
SASA_stdev110.030
SubTypeB
Temperature298K
Topologyf2dgc_nowat.prmtop
Trajectoryf2dgc_nowat.nc
WaterSPCE
_idNAFlex_2dgc
altPDB1DGC 2DGC
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-24
descriptionDNA-B Duplex Complex ParmBSC1 SPC/E AddedSalt Protein-nuc
forceFieldparmBSC1
ionsModel-
moleculeTypeProt-Dna
rev_sequenceGGAGATGACGTCATCTCC
saltConcentration-
sequenceGGAGATGACGTCATCTCC
soluteAtoms2864
soluteCharge-18
soluteResidues134
solventAtoms-
solventResidues-
time1,000
totalAtoms2864
totalCharge-18
totalIons-
totalResidues134
Quality Control
RMSd-
Rgyr-
SASA-
RMSf-