1,721,279 research outputs found
EntF*-D7
No full textmolecular dynamics simulation of the EntF* peptide, residue 7 in D form -starting coordinates posre.gro: energy minimized and water+ions equilibrated around peptide -topology topol.top: force field AMBER99SB-ILDB, TIP3P water, protonation states at pH = 3 (E,K protonated), [NaCl] = 25 mM, disulfide bond generated between residues 14 and 6 -md settings md.mdptime step 2 fs, temperature = 298 K, pressure = 1 bar -1 microsecond trajectory dry.xtc, dry.gro frame rate 10 ps, water and ions removed, box centered on peptide -analysis files: radius of gyration, solvent accessible surface area (hydrophilic (backbone + hydrophilic side chains), hydrophobic (hydrophobic side chains)
EntF*-D10
No full textmolecular dynamics simulation of the EntF* peptide, residue 10 in D form -starting coordinates posre.gro: energy minimized and water+ions equilibrated around peptide -topology topol.top: force field AMBER99SB-ILDB, TIP3P water, protonation states at pH = 3 (E,K protonated), [NaCl] = 25 mM, disulfide bond generated between residues 14 and 6 -md settings md.mdp time step 2 fs, temperature = 298 K, pressure = 1 bar -1 microsecond trajectory dry.xtc, dry.gro frame rate 10 ps, water and ions removed, box centered on peptide -analysis files: radius of gyration, solvent accessible surface area (hydrophilic (backbone + hydrophilic side chains), hydrophobic (hydrophobic side chains)
EntF*-D5
No full textMolecular dynamics simulation of the EntF* peptide, residue 5 in D form -starting coordinates posre.gro energy minimized and water+ions equilibrated around peptide -topology topol.top force field AMBER99SB-ILDB, TIP3P water protonation states at pH = 3 (E,K protonated) [NaCl] = 25 mM disulfide bond generated between residues 14 and 6 -md settings md.mdp time step 2 fs, temperature = 298 K, pressure = 1 bar -1 microsecond trajectory dry.xtc, dry.gro frame rate 10 ps, water and ions removed, box centered on peptide -analysis files frame rate 1 ps radius of gyration, solvent accessible surface area (hydrophilic parts (backbone + hydrophilic side chains), hydrophobic parts (hydrophobic side chains)
EntF*-D14
No full textmolecular dynamics simulation of the EntF* peptide, residue 14 in D form starting coordinates posre.gro: energy minimized and water+ions equilibrated around peptide topology topol.top: force field AMBER99SB-ILDB, TIP3P water, protonation states at pH = 3 (E,K protonated), [NaCl] = 25 mM, disulfide bond generated between residues 14 and 6 md settings md.mdp: time step 2 fs, temperature = 298 K, pressure = 1 bar 1 microsecond trajectory dry.xtc, dry.groframe rate 10 ps, water and ions removed, box centered on peptide analysis files: radius of gyration, solvent accessible surface area (hydrophilic (backbone + hydrophilic side chains), hydrophobic (hydrophobic side chains)
EntF*-D15
No full textmolecular dynamics simulation of the EntF* peptide, residue 15 in D form -starting coordinates posre.gro: energy minimized and water+ions equilibrated around peptide -topology topol.top: force field AMBER99SB-ILDB, TIP3P water, protonation states at pH = 3 (E,K protonated), [NaCl] = 25 mM, disulfide bond generated between residues 14 and 6 -md settings md.mdp time step 2 fs, temperature = 298 K, pressure = 1 bar -1 microsecond trajectory dry.xtc, dry.groframe rate 10 ps, water and ions removed, box centered on peptide -analysis files: radius of gyration, solvent accessible surface area (hydrophilic (backbone + hydrophilic side chains), hydrophobic (hydrophobic side chains)
EntF*-D8
No full textmolecular dynamics simulation of the EntF* peptide, residue 8 in D form -starting coordinates posre.gro: energy minimized and water+ions equilibrated around peptide -topology topol.top: force field AMBER99SB-ILDB, TIP3P water, protonation states at pH = 3 (E,K protonated), [NaCl] = 25 mM, disulfide bond generated between residues 14 and 6 -md settings md.mdp time step 2 fs, temperature = 298 K, pressure = 1 bar -1 microsecond trajectory dry.xtc, dry.gro frame rate 10 ps, water and ions removed, box centered on peptide -analysis files: radius of gyration, solvent accessible surface area (hydrophilic (backbone + hydrophilic side chains), hydrophobic (hydrophobic side chains)
EntF*-D13
No full textmolecular dynamics simulation of the EntF* peptide, residue 13 in D form -starting coordinates posre.gro: energy minimized and water+ions equilibrated around peptide -topology topol.top: force field AMBER99SB-ILDB, TIP3P water, protonation states at pH = 3 (E,K protonated), [NaCl] = 25 mM, disulfide bond generated between residues 14 and 6 -md settings md.mdp time step 2 fs, temperature = 298 K, pressure = 1 bar -1 microsecond trajectory dry.xtc, dry.gro frame rate 10 ps, water and ions removed, box centered on peptide -analysis files: radius of gyration, solvent accessible surface area (hydrophilic (backbone + hydrophilic side chains), hydrophobic (hydrophobic side chains)
EntF*-L
No full textMolecular dynamics simulation of the EntF* peptide, all residues in L form -starting coordinates posre.gro energy minimized and water+ions equilibrated around peptide -topology topol.top force field AMBER99SB-ILDB, TIP3P water protonation states at pH = 3 (E,K protonated) [NaCl] = 25 mM disulfide bond generated between residues 14 and 6 -md settings md.mdp time step 2 fs, temperature = 298 K, pressure = 1 bar -1 microsecond trajectory dry.xtc, dry.gro frame rate 10 ps, water and ions removed, box centered on peptide -analysis files frame rate 1 ps radius of gyration, solvent accessible surface area (hydrophilic parts (backbone + hydrophilic side chains), hydrophobic parts (hydrophobic side chains)
EntF*-D12
No full textmolecular dynamics simulation of the EntF* peptide, residue 12 in D form -starting coordinates posre.gro: energy minimized and water+ions equilibrated around peptide -topology topol.top: force field AMBER99SB-ILDB, TIP3P water, protonation states at pH = 3 (E,K protonated), [NaCl] = 25 mM, disulfide bond generated between residues 14 and 6 -md settings md.mdp time step 2 fs, temperature = 298 K, pressure = 1 bar -1 microsecond trajectory dry.xtc, dry.groframe rate 10 ps, water and ions removed, box centered on peptide -analysis files: radius of gyration, solvent accessible surface area (hydrophilic (backbone + hydrophilic side chains), hydrophobic (hydrophobic side chains)
EntF*-D6
No full textMolecular dynamics simulation of the EntF* peptide, residue 6 in D form -starting coordinates posre.gro energy minimized and water+ions equilibrated around peptide -topology topol.top force field AMBER99SB-ILDB, TIP3P water protonation states at pH = 3 (E,K protonated) [NaCl] = 25 mM disulfide bond generated between residues 14 and 6 -md settings md.mdp time step 2 fs, temperature = 298 K, pressure = 1 bar -1 microsecond trajectory dry.xtc, dry.gro frame rate 10 ps, water and ions removed, box centered on peptide -analysis files frame rate 1 ps radius of gyration, solvent accessible surface area (hydrophilic parts (backbone + hydrophilic side chains), hydrophobic parts (hydrophobic side chains)
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