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6 results for “Alchemical Free Energy”
Alchemical Free Energy Estimators and Molecular Dynamics Engines: Accuracy, Precision and Reproducibility - Dataset
<p>This zip contains all input structures for paper the: Alchemical Free<br> Energy Estimators and Molecular Dynamics<br> Engines: Accuracy, Precision and Reproducibility</p> <p>Authors: Alexander D. Wade, Agastya P. Bhati, Shunzhou Wan, Peter V.Coveney</p> <p>The structures of the folders are protein/ligand_transformation/alchemical_leg/input/files</p> <p>The ligand transformation are derived from previous work by wang et al. (https://pubs.acs.org/doi/10.1021/ja512751q)</p> <p>There are two files for the solvent alchemical leg: complex.pdb and complex.prmtop</p> <p>complex.pdb is structure file that also denotes the alchemical atoms in the pdb beta column. complex.prmtop is an AMBER parameter/topology file</p> <p>For the complex alchemical leg there is an additional file constraints.pdb that contains the constraint information in the pdb beta column.</p> <p>These files can be used with TIES_MD (https://ucl-ccs.github.io/TIES_MD/) or other molecular dynamics engiens that take AMBER input.</p>
Supporting material of "A nonequilibrium alchemical method for drug-receptor absolute binding free energy calculations: the role of restraints"
<p>Supporting material of the paper "A nonequilibrium alchemical method for drug-receptor absolute binding free energy calculations: the role of restraints".</p> <p>The directory is fully documented with README files.</p> <p>Differences of V2.0 with V1.0:</p> <ul> <li>Due to a software bug we had to re-parametrize the ligands whose torsions were parametized with ANI-2.X (ligand 6 and 7).</li> <li>During the peer reviewing process we also parametrized with ANI-2.X and docked ligand 8.</li> </ul>
Data for: Alchemical free-energy calculations at quantum-chemical precision
<p><span><span>In the last decade, machine-learned potentials (MLP) have </span><span>demonstrated</span><span> the capability to predict vario</span><span>us</span><span> QM properties learned from </span><span>a set of reference</span><span> QM calculations. </span><span>Accordingly</span><span>,</span><span> hybrid QM/MM simulation</span><span>s </span><span>can be accelerated</span><span> by replacement of </span><span>expensive</span><span> QM calculation</span><span>s</span><span> with </span><span>efficient </span><span>MLP </span><span>energy prediction</span><span>s</span><span>.</span> <span>At the same time</span><span>, alchemical free energy </span><span>perturbation</span><span>s</span><span> (FEP) </span><span>remain</span> <span>un</span><span>ach</span><span>ie</span><span>vable</span><span> at the QM level of theory.</span> <span>In this work</span><span>,</span><span> we extend the capabilities of the Buffer Region Neural Network </span><span>(</span><span>BuRNN</span><span>) </span><span>QM</span><span>/MM</span><span> scheme towards </span><span>FEP</span><span>.</span> <span>BuRNN</span> <span>introduces a buffer region that experiences full electronic polarization by the QM region to minimize artifacts</span> <span>at </span><span>the </span><span>QM/MM interface</span><span>. </span><span>A </span><span>MLP</span> <span>is </span><span>used to </span><span>predict the energies for the QM </span><span>region</span><span> and its interactions with the buffer region</span><span>. Furthermore, </span><span>BuRNN</span> <span>allow</span><span>s</span><span> us to implement </span><span>FEP </span><span>directly into</span> <span>the </span><span>MLP </span><span>H</span><span>amiltonian</span><span>. </span><span>Here</span><span>, </span><span>we describe the alchemical change </span><span>from methanol to methane in water </span><span>at</span><span> the </span><span>MLP</span><span>/MM level as a proof of concept.</span></span><span> </span></p>
Alchemical Free Energy Estimators and Molecular Dynamics Engines: Accuracy, Precision and Reproducibility
<p>This zip contains all input structures for paper the: Alchemical Free<br> Energy Estimators and Molecular Dynamics<br> Engines: Accuracy, Precision and Reproducibility</p> <p>Authors: Alexander D. Wade, Agastya P. Bhati, Shunzhou Wan, Peter V.Coveney</p> <p>The structures of the folders are protein/ligand_transformation/alchemical_leg/input/files</p> <p>The ligand transformation are derived from previous work by wang et al. (https://pubs.acs.org/doi/10.1021/ja512751q)</p> <p>There are two files for the solvent alchemical leg: complex.pdb and complex.prmtop</p> <p>complex.pdb is structure file that also denotes the alchemical atoms in the pdb beta column. complex.prmtop is an AMBER parameter/topology file</p> <p>For the complex alchemical leg there is an additional file constraints.pdb that contains the constraint information in the pdb beta column.</p> <p>These files can be used with TIES_MD (https://ucl-ccs.github.io/TIES_MD/) or other molecular dynamics engiens that take AMBER input.</p>
Does Hamiltonian Replica Exchange via lambda-hopping enhance the sampling in alchemical binding free energy calculations?
<p>t-REM HREM lamba-hopping/FEP+ tests on the APA molecule with ORAC<br> (www.chim.unifi.it/orac) </p> <p>The untarred archive contains the following directories: </p> <p>t-rem -> contains input for gas-phase tests<br> st-hrem -> contains input for solvated APA with solute tempering<br> lam-hop -> contains input for solvated APA with lambda-hopping<br> bin -> scripts for REM analysis <br> lib -> APA starting conf and potential parameters for the runs </p> <p>see also README files inside each dir for further details </p>
Alchemical Free Energy Estimators and Molecular Dynamics Engines: Accuracy, Precision and Reproducibility - Dataset
<p>This zip contains all input structures for paper the: Alchemical Free<br> Energy Estimators and Molecular Dynamics<br> Engines: Accuracy, Precision and Reproducibility</p> <p>Authors: Alexander D. Wade, Agastya P. Bhati, Shunzhou Wan, Peter V.Coveney</p> <p>The structures of the folders are protein/ligand_transformation/alchemical_leg/input/files</p> <p>The ligand transformation are derived from previous work by wang et al. (https://pubs.acs.org/doi/10.1021/ja512751q)</p> <p>There are two files for the solvent alchemical leg: complex.pdb and complex.prmtop</p> <p>complex.pdb is structure file that also denotes the alchemical atoms in the pdb beta column. complex.prmtop is an AMBER parameter/topology file</p> <p>For the complex alchemical leg there is an additional file constraints.pdb that contains the constraint information in the pdb beta column.</p> <p>These files can be used with TIES_MD (https://ucl-ccs.github.io/TIES_MD/) or other molecular dynamics engines that take AMBER input.</p>
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