PDB files used in the system preparation, AMBER topologies and coordinates and force field parameters for non-standard residues: The Influence of Chemical Change on Protein Dynamics: A Case Study with Pyruvate Formate-Lyase

PDB files used in the system preparation, AMBER topologies and coordinates and force field parameters for non-standard residues: The Influence of Chemical Change on Protein Dynamics: A Case Study with Pyruvate Formate-Lyase

We provide AMBER topology (parm7) and coordinate files (pdb and rst7) for PFL systems before and after the first half-reaction together with library and frcmod files (lib and frcmod) for non-standard residues (bonded and non-bonded force field parameters).mPFL - monomeric PFL system before the first...

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Hauptverfasser: Hanzevacki, Marko, Condic-Jurkic, Karmen, Banhatti, Radha Dilip, Ana-Sunčana Smith, Smith, David Matthew
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creator Hanzevacki, Marko
Condic-Jurkic, Karmen
Banhatti, Radha Dilip
Ana-Sunčana Smith
Smith, David Matthew
description We provide AMBER topology (parm7) and coordinate files (pdb and rst7) for PFL systems before and after the first half-reaction together with library and frcmod files (lib and frcmod) for non-standard residues (bonded and non-bonded force field parameters).mPFL - monomeric PFL system before the first half-reaction (radical on C418)dPFL - dimeric PFL system before the first half-reaction (radical on C418)mAcPFLI - monomeric PFL system after the first half-reaction (radical on formyl)dAcPFLI - dimeric PFL system after the first-half reaction (radical on formyl)mAcPFLII - monomeric PFL system after the first half-reaction (radical on C419)dAcPFLII - dimeric PFL system after the first half-reaction (radical on C419)PYR - pyruvateFOR - CO2- radicalFOH - formateCYR - cysteinyl radicalCYA - S-acetyl-cysteineElectrostatic potentials were derived from the IEF-PCM B3LYP/cc-pVTZ//HF/6-31G(d,p) calculationsm while the atomic partial charges were developed using RESP procedure.
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title PDB files used in the system preparation, AMBER topologies and coordinates and force field parameters for non-standard residues: The Influence of Chemical Change on Protein Dynamics: A Case Study with Pyruvate Formate-Lyase
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