Molecular Modeling and Bioinformatics Group

Nucleic Acid Data:

Sequence	CGTACG
Rev. Sequence	CGTACG
Type	DNA
SubType	B
Chains	duplex
Pdb	1D11 [PDB] [NDB]
Ligands	No
Keywords	DNA-B Duplex Naked ParmBSC1 TIP3P Electroneutral Ligand-intercalator

MD Simulation >> (Click to expand/shrink)

Simulation Metadata
Force Field	parmBSC1
Simulation Date	2015-Apr-21
Simulated Time	1,000 ns
Time Step	100ps
Parts	only DNA
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	duplex
Comments	-
CounterIons	Na+
Format	mdcrd
FrameStep	100ps
Frames	10001
IonicConcentration	Electroneutrality
IonsParameters	Dang
Ligands	No
NucType	DNA
PDB	1D11
Parts	only DNA
RMSd_avg	1.765
RMSd_stdev	0.504
Rgyr_avg	9.399
Rgyr_stdev	0.176
SASA_avg	2626.773
SASA_stdev	55.803
SubType	B
Temperature	300K
Topology	intercalator.onlydna.top
Trajectory	intercalator.onlydna.trj.gz
Water	TIP3P
_id	NAFlex_1d11
altPDB	1AO1 1C9Z 1D11 1D14 1D17 1D21 1D22 1D35 1D36 1DL8 1FD5 1FDG 1FN2 1K2J 1K2K 1K2L 1KCI 1M69 1RQY 1UQE 1VTG 1VTW 1XCS 1XCU 1XVR 210D 211D 215D 288D 2D34 2DES 2ET0 2GB9 2GJB 308D 386D 3FX8 3I1D 3NP6 3NX5 452D 465D 4D9X 4D9Y 4GQJ 4MNB
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-Apr-21
description	DNA-B Duplex Naked ParmBSC1 TIP3P Electroneutral Ligand-intercalator
forceField	parmBSC1
ionsModel	-
moleculeType	Dna
rev_sequence	CGTACG
saltConcentration	-
sequence	CGTACG
soluteAtoms	378
soluteCharge	-10
soluteResidues	12
solventAtoms	-
solventResidues	-
time	1,000
totalAtoms	378
totalCharge	-10
totalIons	-
totalResidues	12