gromos 53a6 force field

It makes use of the united atom approach for aliphatic hydrogens. Comparisons of the herein presented parameter set to our previous version (GROMOS 45A4), the GLYCAM06 force field, and available NMR data are presented in terms of ring puckering free energies, conformational distribution of the hydroxymethyl group, and glycosidic linkage . These parameter sets summarise some previously published force field modifications: The 53A6 helical propensities are corrected through new φ/ψ torsional angle terms and a modification of the N-H, C=O repulsion, a new atom type for a charged -CH(3) in the choline moiety is added, the Na(+) and Cl . without explicit aliphatic (non-polar) hydrogens. J. Chem. 2005 ). Total number of atoms: 16853. This article presents a reoptimization of the GROMOS 53A6 force field for hexopyranose-based carbohydrates (nearly equivalent to 45A4 for pure carbohydrate systems) into a new version 56A(CARBO) (nearly equivalent to 53A6 for non-carbohydrate systems). Force field comparison: Amber, GROMOS, CHARMM, OPLS: Comparison of secondary structure formation using different force fields in microsecond molecular dynamics simulations. What I ultimately want is just the gromacs input topology files etc. The recently developed GROMOS 54A7 force field, a modification of the 53A6 force field, is validated by simulating the folding equilibrium of two β-peptides which show different dominant folds, i.e., a 314-helix and a hairpin, using three . T1 - A biomolecular force field based on the free enthalpy of hydration and solvation. g_rms, r_gyrate, and g_hbond plugins of Gromacs were used to analyze . Additional features include two similar minima in the α + basin. For the purposes of the rest of this work, the ssDNA sequence will be referred to as follows: To investigate the transferability of the new parameter set, we calculated free enthalpies of solvation of a range of polar and apolar compounds in . The GROMOS force field is compatible with the simple point charge (SPC) water model. I . Chem. 37 (2016) 354-365, DOI: 10.1002/jcc.24229 ===== Changes in force-field files (May 24, 2013) generation of the GROMOS force ﬁeld the polar amino acid side-chains and peptide backbone moiety were repara-metrised. I want to use the more recent carbohydrate specific 53a6_carbo force field. Read 3 answers by scientists to the question asked by Swapnil Wagle on Feb 5, 2016 2004 vol 25 pag 1656) in gromacs format. A short summary of this paper. All parameters for the 43A1, 43A2 (development, improved alkane dihedrals), 45A3, 53A5, and 53A6 parameter sets are included. From time to time a new version is brought out. 2003; 66:27-85. Download Full PDF Package. W. Plazinski, A. Lonardi, and P.H. Oostenbrink C, Villa A, Mark AE, van Gunsteren WF (2004) A biomolecular force field based on the free enthalpy of hydration and solvation: the GROMOS force-field parameter sets 53A5 and 53A6. We also have simulated the XAO peptide by using the GROMOS 53A6 force field and the gromos md package (47, 48) on a Pentium cluster.Nonbonded interactions were treated by using a triple range scheme with 8- and 14-Å cutoffs (for details, see ref. Functional Form Download Full PDF Package. [Google Scholar] Ponder JW, Case DA. Original GROMOS Force Field files for use with GROMACS; GROMOS_54A7 . Extension and validation of the GROMOS 53A6(GLYC) parameter set for glycoproteins. once using Gromos 53a6 and its parametrized water model (SPC, I guess) to estimate free energies and the second time using another force field which will not result in instability! I want to . Crossref; PubMed ; Scopus (2771) Google Scholar) The initial system consisted of the α-HL barrel embedded in a ∼1000 . 25 (13): 1656-1676). The set includes new atomic charges and incorporates adequate . Assuming that NMA represents an adequate model . For example, the CHARMM and OPLS FFs exhibit lower average β-sheet content in dimers of Aβ42 than that obtained with GROMOS 53a6 force field [18]. Subsequently, the average β-sheet content of the Aβ42 dimers was found to be greater in OPLSAA [19] than in AM- BERFF99SB [20]. KW - force-field parameterization. P3HT and PCBM atomistic force fields By Riccardo Alessandri (4043948), Jaakko J. Uusitalo (3816010), Alex H. de Vries (226821), Remco W. A. Havenith (1374558) and Siewert J. Marrink (135518) Cite The 54A7 force field stabilizes both folds, and the agreement of the simulated NOE atom-atom . MD simulation of a DMPC bilayer: 200 ns Gromos 53A6 force field and Berger lipids (lipid.itp) 128 DMPC lipids and 3655 SPC waters. Even though the charges on the nucleotide sugars and bases have not changed in the 53A6 parameter set, the van der Waals Other parameters, as the rules for third and excluded neighbors, are taken directly from the GROMOS 53A6 force field. Interestingly, both AMBER99SB-ILDN and OPLS/L FFs have produced results of the average secondary structure of Aβ42 . To investigate the transferability of the new parameter set, we calculated free enthalpies of solvation of a range of polar and apolar compounds in . 2004, 25 (13): 1656-1676. Abstract Recently, the GROMOS biomolecular force field parameter set 53A6—which has been parametrized to reproduce experimentally determined free enthalpies of hydration and solvation in cyclohexan. Here is a brief summary of my situation: >From what my copy of gromacs tells me pdb2gmx is using a 53a6 forcefield from 2004. As a final step, MDSs were performed for 50 ns and trajectories were obtained. A draft description of the GROMOS force field by the IGC group at ETH, Zurich is given here. 46).The electrostatic interactions were treated by using the reaction-field method with a cutoff of 14 Å and dielectric . Please let me know your point of view . The simple point charge (SPC) model was selected for water molecules. These parameter sets summarise some previously published force field modifications: The 53A6 helical propensities are corrected through new φ/ψ torsional angle terms and a modification of the N-H, C=O repulsion … Comput., 2016, 12, 3825−3850 ; The 2016H66 files in GROMOS format are . Download PDF. An extension of the GROMOS 53A6GLYC force field for carbohydrates to encompass glycoprotein linkages is presented. AU - van Gunsteren, W.F. GROMOS 53A6 IFP files with additions from the ATB ; GROMOS11 54a7 ATB.ifp: GROMOS96 ifp54a7 ATB.dat: Additional GROMOS forcefield files can be found here. A biomolecular force field based on the free enthalpy of hydration and solvation: The GROMOS force‐field parameter sets 53A5 and 53A6 - Oostenbrink - 2004 - Journal of Computational Chemistry - Wiley Online Library Journal of Computational Chemistry Recently, the GROMOS biomolecular force field parameter set 53A6—which has been parametrized to reproduce experimentally determined free enthalpies of hydration and solvation in cyclohexane of amino acid side-chain analogs—was presented. New parameter sets of the GROMOS biomolecular force field, 54A7 and 54B7, are introduced. 1998) and a limited set of different atom types, bond types, bond-angle types, improper dihedral types and torsional-angle types. GROMOS 45a3 forcefield, specified by -ff G45a3 and it works great. This paper. GROningen MOlecular Simulation (GROMOS) is the name of a force field for molecular dynamics simulation, and a related computer software package. In this way we can ensure our results are more precise. An Automated Force Field Topology Builder (ATB) and Repository: Version 1.0. 12 Pages. Evaluation of the GROMOS 56ACARBO Force Field for the Calculation of Structural, Volumetric, and Dynamic Properties of Aqueous Glucose Systems Marta L. S. Batista,†,‡ GermanPé rez-Sá nchez,́ † JoséR. J Comput Chem 25: 1656-1676. 54A7 (taken 53A6 and adjusted torsional angle terms to better reproduce helical propensities, altered N-H, C=O repulsion, new CH3 charge group, parameterisation of Na+ and Cl- to improve free eneergy of hydration and new improper dihedrals) - Schmid N., Eichenberger A., Choutko A., Riniker S., Winger M., Mark A. Chem. while van der Waals and dihedral parameters were modified from 43A1 to improve . Simulations used the GROMOS 53A6 force field (23. Rather, short α-helices were found to be less stable than expected. Personally, I have been and am still suspicious regarding these newer force fields, possibly with the exception of 54a8. The recently developed GROMOS 54A7 force field, a modification of the 53A6 force field, is validated by simulating the folding equilibrium of two β-peptides which show different dominant folds, i.e., a 314-helix and a hairpin, using three different force fields, i.e., GROMOS 45A3, 53A6, and 54A7. Alan Mark. Functional Form In a classical molecular dynamics simulation, all degrees of free- dom that are treated explicitly are . Both are developed at the University of Groningen, and at the Computer-Aided Chemistry Group at the Laboratory for Physical Chemistry at the Swiss Federal Institute of Technology ( ETH Zurich ). New parameter sets of the GROMOS biomolecular force field, 54A7 and 54B7, are introduced. In 2006 I performed a statistical comparison of simulations performed with 43a2 . 25196137. The transition region connecting α R and γ is slightly more prominent in the longer Ala 7, along with a more pronounced γ region . This reoptimization was found necessary to repair a number of shortcomings of the 53A6 (45A4) parameter set and to extend the scope of the . The GROMOS Force-Field Parameter Sets1657 will ease the use of this latest GROMOS parameterization, because in the 53A5 and 53A6 parameter sets many interactions types have been redeﬁned, and all types have been renumbered with respect to the previous parameter sets. 2004 vol. Simulation details: Temperature: 323 K Times step: 2 fs V-rescale thermostat, Parrinello-Rahman barostat, P-LINCS for constraints The run was done using a . Chem. However, the GRO-MOS 53A6 force ﬁeld, in which the hydration properties of amino acid analogues are in good agreement with experi- An Automated Force Field Topology . However, the GRO-MOS 53A6 force ﬁeld, in which the hydration properties of amino acid analogues are in good agreement with experi- J Comput Chem. This reoptimization was found necessary to repair a number of shortcomings of the 53A6 (45A4) parameter set and to extend the scope of the . 37 Full PDFs related to this paper. 1999; van Gunsteren et al. This simulation: 200 ns. This paper. The problem of amine hydration and the inaccuracy . The resulting set, referred to as 53A6(OXY+A) , represents an improvement over earlier GROMOS force-field versions in the context of the pure-liquid properties of NMA, including the density, heat of vaporization, dielectric permittivity, self-diffusion constant and viscosity, as well as in terms of the Gibbs hydration free energy of this molecule. Journal of Computational Chemistry 2014 November 5, 35 (29): 2087-95. 04 February 2016 3 8K Report. Force fields, which are generally parameterized using experimental data on small molecules, can only prove themselves in realistic simulations of relevant biomolecular systems. The GROMOS-96 force field is a further development of the GROMOS-87 force field. READ PAPER. & van Gunsteren W., Definition and testing of the GROMOS force-field versions . View Article Google Scholar 22. To investigate the transferability of the new parameter set, we calculated free enthalpies of solvation of a range of polar and apolar compounds in . The set includes new atomic charges and incorporates adequate torsional potential parameters for N-, S-, C-, P-, and O-glycosydic linkages, offering compatibility with the GROMOS force … Extension and validation of the GROMOS 53A6(GLYC) parameter set for glycoproteins J Comput . J. Comput. A GROMOS-Compatible Force Field for Small Organic Molecules in the Condensed Phase: The 2016H66 Parameter Set Bruno A. C. Horta,*,†,§ Pascal T. Merz,† Patrick F. J. Fuchs,∥ Jozica Dolenc,†,‡ Sereina Riniker,† and Philippe H. Hünenberger† † Laboratory of Physical Chemistry, ETH Zürich, CH-8093 Zürich, Switzerland Chemistry, Biology and Pharmacy Information Center, ETH . The files of the GROMOS-compatible 2016H66 force field are available for download in the table below. This article presents a reoptimization of the GROMOS 53A6 force field for hexopyranose-based carbohydrates (nearly equivalent to 45A4 for pure carbohydrate systems) into a new version 56A(CARBO) (nearly equivalent to 53A6 for non-carbohydrate systems). 116 All the other force fields rely on the three-point transferable intermolecular potential (TIP3P) model, 117,118 further labelled TP3. The historic sequence of GROMOS force ﬁelds is the following: - the 26C1 force ﬁeld of June 1981 - the 37C2 (and 37D2) force ﬁeld(s) of January 1983 (extended in November 1983) - the 37C4 (and 37D4) force ﬁeld(s) of November 1983 (revised in December 1985 . Laercio Pol-Fachin, Hugo Verli, Roberto D Lins . This resulted in the GROMOS 53A6 parameter set (Oostenbrink et al. generation of the GROMOS force ﬁeld the polar amino acid side-chains and peptide backbone moiety were repara-metrised. Reference: B.A.C. generated by pdb2gmx (or some other equivalent application). I have the force field parameters for the lipid as well as for the peptide, but not for the linker (which is a molecular fragment prepared in the lab to link the peptide with the lipid). In addition, C7 ax is not well-populated with the Gromos 53a6 force field. I have a system with lipid-linker-peptide. The GROMOS force fields are united atom force fields, i.e. A short summary of this paper . The systems was equilibrated for 52 ns before this run. Y1 - 2004. 2004; 25 (13):1656-1676. Simulations used the GROMOS 53A6 force field The initial system consisted of the α-HL barrel embedded in a ∼1000-atom methane slab, with one ssDNA dodecamer of sequence 5′-ACCGACGTCGGT-3′ prethreaded into the pore by the first two bases (5′ end) to overcome the energetic barrier to pore entry. Energy minimization and equilibrations (NVT and NPT) were carried out for 100 and 1000 ps, respectively. 2004 vol. These files were used to calculate the solvation free-energy for amino-acid side chains and in protein simulations. Download PDF. The system was neutralized by replacing six water molecules with six Na + ions. This model is also adopted as a usual choice for OPLS-AA, although the force field was originally parametrized using the four-site TIP4P water model 117,118 instead . 43A1-S3 is an extension and modification of the 43A1 force field designed to improve the properties of lipid membranes in simulations. Fuchs, J. Dolenc, S. Riniker & P.H. An Automated Force Field Topology Builder (ATB) and Repository: Version 1.0. European Biophysics Journal, 2011. Recently, the GROMOS biomolecular force field parameter set 53A6--which has been parametrized to reproduce experimentally determined free enthalpies of hydration and solvation in cyclohexane of amino acid side-chain analogs--was presented. GROMACS supports the GROMOS force fields, with all parameters provided in the distribution for 43a1, 43a2, 43b1, 45a3, 53a5 and 53a6. If its working for GROMOS96 53a6 force field then plz write full command for above for filed. Force fields for protein simulations. Chris Oostenbrink 1 , Alessandra Villa 2 , Alan E. Mark 2 , Wilfred F. van Gunsteren 1 • Institutions ( 2 ) Theory. This article presents a reoptimization of the GROMOS 53A6 force field for hexopyranose-based carbohydrates (nearly equivalent to 45A4 for pure carbohydrate systems) into a new version 56A(CARBO) (nearly equivalent to 53A6 for non-carbohydrate systems). The hydration of the polymer depends largely on the nature of the polar groups in the chain. We also have simulated the XAO peptide by using the GROMOS 53A6 force field and the gromos md package (47, 48) on a Pentium cluster. Hünenberger. Comparisons of the herein presented parameter set to our previous version (GROMOS 45A4), the GLYCAM06 force ﬁeld, and available NMR data are presented in terms of ring puckering free energies, conformational distribution of the hydroxymethyl group, and glycosidic linkage . The GROMOS Force-Field Parameter Sets 1657. will ease the use of this latest GROMOS parameterization, because in the 53A5 and 53A6 parameter sets many interactions types have been redeﬁned, and all types have been renumbered with respect to the previous parameter sets. This reoptimization was found necessary to repair a number of shortcomings of the 53A6 (45A4) parameter set and to extend the scope of the . Gromos 53a6 force field: How to calculate partial atomic charges for a molecular fragment? The GROMOS 53a6 force field (see J. Comput. N1 - J CT. PY - 2004. However, the GROMOS 53A6 force field, in which the hydration properties of amino acid analogues are in good agreement with experiment, did not improve the stability of the dominant fold for all peptides (Oostenbrink et al. T2 - The GROMOS force-field parameter sets 53A5 and 53A6. 2004; 25: 1656-1676. Hunenberger, Revision of the GROMOS 56A6CARBO force field: Improving the description of ring-conformational equilibria in hexopyranose-based carbohydrates chains, J Comput. GROMOS parameter set, 45A4, has been introduced, with which it proved possible to obtain a stable simu-lation of this B-DNA double helix using a simple force ﬁeld and cutoﬀ scheme (Soares et al. All standard building blocks are included and topologies can be built automatically by pdb2gmx. 2004, 2005). These parameter sets summarise some previously published force field modifications: The 53A6 helical propensities are corrected through new φ/ψ torsional angle terms and a modification of the N-H, C=O repulsion, a new atom type for a charged -CH(3) in the choline moiety is added, the Na(+) and Cl . This force field was shown to reproduce. The GROMOS 54A7 force field developed to improve the stability of α-helical structures in proteins can thus be safely used in simulations of β-peptides. GROMACS Files. In this case, the secondary amines present on the backbone control the solvation behavior of these vinyl amine polymers in water. GROMACS supports the GROMOS-96 force fields 77. Adv Protein Chem. 43A1-S3 employs charges from Chiu et al. AU - Mark, A.E. These parameter sets summarise some previously published force field modifications: The 53A6 helical propensities are corrected through new φ/ψ torsional angle terms and a modification of the N-H, C=O repulsion, a new atom type for a charged −CH3 in the choline moiety is added, the Na+ and Cl− . KW - GROMOS force field. Oostenbrink C. Villa A. van Gunsteren W.F. Read Paper . The GROMOS 53a6 force field was used. Chem. without explicit aliphatic (non-polar) hydrogens. The recently developed GROMOS 54A7 force field, a modification of the 53A6 force field, is validated by simulating the folding equilibrium of two β-peptides which show different dominant folds, i.e., a 3 14 -helix and a hairpin, using three different force fields, i.e., GROMOS 45A3, 53A6, and 54A7. GROMOS 53a6 - in GROMACS format (J. Comput. Oostenbrink C, Villa A, Mark A, Van Gunsteren W: A biomolecular force field based on the free enthalpy of hydration and solvation: The GROMOS force-field parameter sets 53A5 and 53A6. The 53A6 GLYC [15] force field was used both to validate the sialic acid conformation and use it to propose conformational preferences of higher units. The GROMOS force field is still a force field with a simple functional form (Scott et al. GROMOS 53a6 - in GROMACS format ( J. Comput. Of course it will cost more time. The GROMOS force ﬁeld is continuously being tested and, if necessary, improved. The GROMOS force fields are united atom force fields, i.e. Several GROMOS parameters are used in membrane simulations, such as 43A1-S3 , 53A6 , and Kukol's modification of the 53A6 parameters . Graphene Oxide Force Fields GROMOS Gromacs Molecular Dynamics Molecular Dynamics Simulation Get help. Recently, the GROMOS biomolecular force field parameter set 53A6—which has been parametrized to reproduce experimentally determined free enthalpies of hydration and solvation in cyclohexane of amino acid side‐chain analogs—was presented. Uploaded 13:19 August 30, 2004 by Alessandra Villa (villa at theochem.uni-frankfurt.de) 58.44 kB: 10 . The force field parameters of oil droplet composition were generated by the Automated Topology Builder (ATB) [ 37 , 38 ]. The later GROMOS forcefields 53a5, 53a6, 54a7 and 54a8, took of a completely different approach in parameterization, and are in that respect not so much superseding, but rather complementary. New parameter sets of the GROMOS biomolecular force field, 54A7 and 54B7, are introduced. 10.1002/jcc.20090. Chem. GROMOS 53a6 force field was employed for the topology building. All simulations were started from the same initial conditions. 2004, 2005). B. Gomes,† João A. P. Coutinho, † and Edward J. Maginn*,‡ †Departamento de Química, CICECO, Universidade de Aveiro, Campus Universitario de Santiago, 3810-193 Aveiro, Portugaĺ . Alan Mark. Horta, P.T. AU - Oostenbrink, C. AU - Villa, Alessandra. As observed previously, 48 the Gromos force field exhibits a broader minimum in the ppII region and a subdued C5 minimum. GROMOS simulations. Swapnil Wagle @Swapnil-Wagle. I have only managed to find this force field in GROMOS format. 37 Full PDFs related to this paper. Definition and testing of the GROMOS force-field versions 54A7 and 54B7. The GROMOS 53A6 force-field has been developed to reproduce the solvation (hydration) enthalpy values of amines [54, 55]. Please check them before using them in particular if you simulate not-protein systems. KW - free-energy . How if we simulate our system twice? GROMOS simulations. Nonbonded interactions were treated by . A biomolecular force field based on the free enthalpy of hydration and solvation: the GROMOS force-field parameter sets 53A5 and 53A6. Merz, P.F.J. GROMACS supports the GROMOS force fields, with all parameters provided in the distribution for 43a1, 43a2, 45a3, 53a5, 53a6 and 54a7. Journal of Chemical Theory and Computation, 2011. et al. Oostenbrink C, Villa A, Mark A, Van Gunsteren W. A biomolecular force field based on the free enthalpy of hydration and solvation: The GROMOS force-field parameter sets 53A5 and 53A6. Other parameters, as the rules for third and excluded neighbors, are taken directly from the GROMOS 53A6 force ﬁeld. Force field organization has changed completely since the 4.0.x series; the proper name is now gromos45a3 . In this work, we begin the validation of the new 53A6 GROMOS parameter set by examining three test cases. 25 (13): 1656-1676 ). We have carried out 10 independent simulations starting from the extended PPII configuration for 31.5 ns each, in explicit single point charge water (). The literature reference for the GROMOS 53A6 force field is here. This resulted in the GROMOS 53A6 parameter set (Oostenbrink et al. A biomolecular force field based on the free enthalpy of hydration and solvation: the GROMOS force-field parameter sets 53A5 and 53A6. pdb2gmx -f na.0.pdb -o na_initial.0.gro -ff G45a3 -water spce However, when I move the script to a Mac OS X 10.6 machine running Could not find force field 'G45a3' in current directory, install tree, or GMXDATA path. An extension of the GROMOS 53A6GLYC force field for carbohydrates to encompass glycoprotein linkages is presented. PubMed CAS Article Google Scholar We tested the following force fields: Amber ff99SB-ILDN, Amber ff99SB*-ILDN, Amber ff99SB, Amber ff99SB*, Amber ff03, Amber ff03*, GROMOS96 43a1p, GROMOS96 53a6 . J Comput Chem. A GROMOS-compatible force field for small organic molecules in the condensed phase: The 2016H66 parameter set. 2005). New parameter sets of the GROMOS biomolecular force field, 54A7 and 54B7, are introduced. Molecules with six Na + ions ns and trajectories were obtained to calculate the free-energy! 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[ Google Scholar ) the initial system consisted of the GROMOS-87 force field 54A7 - GROMOS force designed. 54A7... < /a > GROMOS simulations force field based on the backbone control the behavior... Were found to be less stable than expected to use the more recent carbohydrate specific 53a6_carbo force 54A7. Format are ; van Gunsteren W., Definition and testing of the new GROMOS. The united atom approach for aliphatic hydrogens it makes use of the depends. Of the new 53A6 GROMOS parameter set parameter set ( Oostenbrink et al in! This work, we begin the validation of the GROMOS force fields, i.e protein simulations in water potential TIP3P! Dynamics Simulation Get help condensed phase: the GROMOS force fields GROMOS GROMACS Molecular Dynamics Molecular Dynamics Get!, all degrees of free- dom that are treated explicitly are and )... > force field is a further development of the polar groups in the 56A6CARBO... And Repository: version 1.0: version 1.0, 12, 3825−3850 ; the 2016H66 files in GROMOS.., all degrees of free- dom that are treated explicitly are and 1000 ps respectively. It makes use of the α-HL barrel embedded in a classical Molecular Dynamics Simulation, all degrees of free- that..., I have only managed to find this force field for small organic molecules in GROMOS. And equilibrations ( NVT and NPT ) were carried out for 100 and 1000,. 46 ).The electrostatic interactions were treated by using the reaction-field method with cutoff. Riniker & amp ; van Gunsteren W., Definition and testing of the GROMOS 53A6 - in GROMACS (... Get help interestingly, both AMBER99SB-ILDN and OPLS/L FFs have produced results of the polar groups in chain. Present on the nature of the GROMOS force-field versions biomolecular Simulation: free GROMOS simulations ( 2771 ) Google Scholar ) the initial system consisted of 43A1., we begin the validation of the simulated NOE atom-atom, 3825−3850 ; the 2016H66 files in GROMOS format force!: 2087-95 GROMACS Molecular Dynamics Molecular Dynamics Simulation, all degrees of free- dom that are treated explicitly are initial... Jw, case DA 2016H66 files in GROMOS format in this way can!, 117,118 further labelled TP3 model, 117,118 further labelled TP3 Dolenc, S. Riniker & amp ; P.H theochem.uni-frankfurt.de!
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