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SwissParam - Topology and parameters for small organic moleculesDetermine topology and parameters for small organic molecules, for use with CHARMM or GROMACS
http://www.swissparam.ch/
Determine topology and parameters for small organic molecules, for use with CHARMM or GROMACS
http://www.swissparam.ch/
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SwissParam - Topology and parameters for small organic molecules | swissparam.ch Reviews
https://swissparam.ch
Determine topology and parameters for small organic molecules, for use with CHARMM or GROMACS
swissparam.ch
SwissParam - Topology and parameters for small organic molecules
http://www.swissparam.ch/SwissParam_mol2_file.html
Swiss Institute of Bioinformatics. How to obtain a correct mol2 file? Please, note that the mol2 files submitted to SwissParam should contain all the hydrogen atoms. First of all, try the mol2 file you already have. Most of the mol2 files will work, whatever their origin. If one fails, you can try one of the following:. Get it from the ZINC Database. If the molecule is already known,. Or, if the molecule comes from a PDB file (e.g. a ligand), you can use the UCSF chimera. To go back to SwissParam.
SwissParam - Topology and parameters for small organic molecules
http://www.swissparam.ch/SwissParam_gromacs_tutorial.html
Swiss Institute of Bioinformatics. How to set up a GROMACS simulation with a molecule parametrized in SwissParam. Created and maintained by the Molecular modeling group. This tutorial shows how to use SwissParam. To setup a molecular dynamics simulation of a protein with a small-molecule ligand in GROMACS. Forcefield. When using the CHARMM forcefield in GROMACS, please cite [1]. When using SwissParam, pleace cite [2]. Open the ligand raw.pdb file in UCSF Chimera. Then run the pdb2gmx program from the GRO...
SwissParam - Topology and parameters for small organic molecules
http://www.swissparam.ch/citations.html
Swiss Institute of Bioinformatics. Scientific papers citing the SwissParam web server:. Margreitter, C. Petrov, D. Zagrovic, B. Vienna-PTM web server: a toolkit for MD simulations of protein post-translational modifications. Nucleic Acids Res. 2013. Tou, W. I. Chang, S.-S. Lee, C.-C. Chen, C. Y.-C. Drug Design for Neuropathic Pain Regulation from Traditional Chinese Medicine. Sci. Rep. 2013, 3. Otero, J. M. Fernández, F. Estévez, J. C. Nash, R. Estévez, R. J. A Nitro Sugar...Tuffery, P. Derreumaux, P...
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SwissSidechain - A database of non-natural sidechains
http://ns300183.ovh.net/FAQ.php
In order to avoid security-related warning messages when switching to secured connection, you may want either to:. Confirm the exception on the next page, or. Import our CA key. In your web browser. Swiss Institute of Bioinformatics. What is an amino acid? What is a sidechain? What are non-natural sidechains? What is the difference between L and D amino acids? How were the rotamer libraries generated in SwissSidechain? What kind of data can I find in the SwissSidechain database? Where can I obtain PyMOL?
SwissSidechain - A database of non-natural sidechains
http://ns300183.ovh.net/visualization/chimera.php
In order to avoid security-related warning messages when switching to secured connection, you may want either to:. Confirm the exception on the next page, or. Import our CA key. In your web browser. Swiss Institute of Bioinformatics. SwissSidechain - UCSF Chimera Module. This module enables users to mutate any residue of a PDB structure into one of the non-natural L- or D-sidechains of the SwissSidechain database. If you do not have UCSF Chimera, it can be obtained here. Installation (Chimera 1.5 ).
SwissSidechain - A database of non-natural sidechains
http://www.swisssidechain.ch/visualization/chimera.php
In order to avoid security-related warning messages when switching to secured connection, you may want either to:. Confirm the exception on the next page, or. Import our CA key. In your web browser. Swiss Institute of Bioinformatics. SwissSidechain - UCSF Chimera Module. This module enables users to mutate any residue of a PDB structure into one of the non-natural L- or D-sidechains of the SwissSidechain database. If you do not have UCSF Chimera, it can be obtained here. Installation (Chimera 1.5 ).
SwissSidechain - A database of non-natural sidechains
http://www.swisssidechain.ch/visualization.php
In order to avoid security-related warning messages when switching to secured connection, you may want either to:. Confirm the exception on the next page, or. Import our CA key. In your web browser. Swiss Institute of Bioinformatics. SwissSidechain - Visualization Plugins. Swiss Institute of Bioinformatics.
SwissSidechain - A database of non-natural sidechains
http://www.swisssidechain.ch/visualization/pymol.php
In order to avoid security-related warning messages when switching to secured connection, you may want either to:. Confirm the exception on the next page, or. Import our CA key. In your web browser. Swiss Institute of Bioinformatics. SwissSidechain - PyMOL Plugin. This plugin enables you to mutate any residue of a PDB structure into one of the non-natural L- or D-sidechains of the SwissSidechain database. If you do not have PyMOL, it can be obtained here. In a directory of your choice. Copy PySwissSidech...
SwissSidechain - A database of non-natural sidechains
http://www.swisssidechain.ch/D_residues.php
In order to avoid security-related warning messages when switching to secured connection, you may want either to:. Confirm the exception on the next page, or. Import our CA key. In your web browser. Swiss Institute of Bioinformatics. SwissSidechain - D-amino acids. Here, we provide all data to work with both natural and non-natural D-amino acids. All D-amino acids can be accessed from this page. By selecting the corresponding L-form. We note that depending on the backbone dihedral angles (φ and ψ...
SwissSidechain - A database of non-natural sidechains
http://www.swisssidechain.ch/license.php
In order to avoid security-related warning messages when switching to secured connection, you may want either to:. Confirm the exception on the next page, or. Import our CA key. In your web browser. Swiss Institute of Bioinformatics. Access to these database is free for academic use. Access by commercial entities is subject to the licensing conditions outlined in the User Notice ( PDF. And the SIB License ( PDF. Please read the SIB Database Legal Disclaimer. Swiss Institute of Bioinformatics.
SwissSidechain - A database of non-natural sidechains
http://www.swisssidechain.ch/FAQ.php
In order to avoid security-related warning messages when switching to secured connection, you may want either to:. Confirm the exception on the next page, or. Import our CA key. In your web browser. Swiss Institute of Bioinformatics. What is an amino acid? What is a sidechain? What are non-natural sidechains? What is the difference between L and D amino acids? How were the rotamer libraries generated in SwissSidechain? What kind of data can I find in the SwissSidechain database? Where can I obtain PyMOL?
SwissSidechain - A database of non-natural sidechains
http://www.swisssidechain.ch/MD.php
In order to avoid security-related warning messages when switching to secured connection, you may want either to:. Confirm the exception on the next page, or. Import our CA key. In your web browser. Swiss Institute of Bioinformatics. SwissSidechain - Molecular Dynamics. You can find here topologies and parameters for molecular mechanics simulations with non-natural sidechains in GROMACS and CHARMM. Swiss Institute of Bioinformatics.
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SwissParam - Topology and parameters for small organic molecules
In order to avoid security-related warning messages when switching to secured connection, you may want either to:. Confirm the exception on the next page, or. Import our CA key. In your web browser. Swiss Institute of Bioinformatics. This service provides topology and parameters for small organic molecules compatible with the CHARMM all atoms force field, for use with CHARMM and GROMACS. Created and maintained by the Molecular modeling group. SwissParam is automatically used by SwissDock. V Zoete, M....
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