Molecular Modeling and Bioinformatics Group

Nucleic Acid Data:

Sequence 1:	CCGGTACCGG
Sequence 2:	CCGGTACCGG
Sequence 3:	CCGGTACCGG
Type	DNA
SubType	B
Chains	Holliday Junction
Pdb	1DCW [PDB] [NDB]
Ligands	No
Keywords	DNA-B HollidayJunction Naked ParmBSC1 TIP3P Electroneutral 4way-junction inverted-repeat

MD Simulation >> (Click to expand/shrink)

Simulation Metadata
Force Field	parmBSC1
Simulation Date	2015-May-05
Simulated Time	1,000 ns
Time Step	100ps
Parts	DNA/DNA+ions
Temperature	300K
Water	TIP3P
Additional Solvent	No
Counter Ions	Na+
Ionic Concentration	Electroneutrality
Additional Ions	No
Additional Molecules	No
Ions Parameters	Dang

Unified Molecular Modeling (UMM) Metadata
(Click to see full UMM)

Simulation Metadata (UMM)
AdditionalIons	No
AdditionalMolecules	No
AdditionalSolvent	No
Author	I.F.
Chains	Holliday Junction
Comments	-
CounterIons	Na+
Format	mdcrd
FrameStep	100ps
Frames	10001
IonicConcentration	Electroneutrality
IonsParameters	Dang
Ligands	No
NucType	DNA
PDB	1DCW
Parts	DNA/DNA+ions
RMSd_avg	3.051
RMSd_stdev	0.581
Rgyr_avg	14.772
Rgyr_stdev	0.429
SASA_avg	6763.881
SASA_stdev	219.414
SubType	B
Temperature	300K
Topology	holliday.vac.top/holliday.helixI.top/holliday.helixII.top
Trajectory	holliday.helixI.trj/holliday.helixII.trj/holliday.helixIions.trj.gz
Water	TIP3P
_id	NAFlex_1dcw
altPDB	1DCW 1FHZ 1JUC 1L6B 1NT8 1NVN 1ZEZ 3HS1 3IXN 3R86 3U38 3UYA 4M3I 4R48 4R49 4R4A 4R4D
authors	Ivan 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
dataset	Array
date	2015-May-05
description	DNA-B HollidayJunction Naked ParmBSC1 TIP3P Electroneutral 4way-junction inverted-repeat
forceField	parmBSC1
ionsModel	-
moleculeType	Dna
rev_sequence	CCGGTACCGG
saltConcentration	-
sequence	CCGGTACCGG \| CCGGTACCGG \| CCGGTACCGG
sequenceMulti	Array
soluteAtoms	1260
soluteCharge	-36
soluteResidues	40
solventAtoms	-
solventResidues	-
time	1,000
totalAtoms	1260
totalCharge	-36
totalIons	-
totalResidues	40