charmm-gui.org

CHARMM-GUI

CHARMM is a versatile program for atomic-level simulation of. Many-particle systems, particularly macromolecules of. Biological interest. - M. Karplus. Are now available. See upload log. For update history and giving. For donation. Contact. Info is given below. CHARMM-GUI is powered by CHARMM, an academic research program used world-wide for macromolecular dynamics and mechanics ( http:/ www.charmm.org. Academic users can obtain CHARMM freely from http:/ www.charmm.org. Department of Biological Sciences.

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CONTACTS AT CHARMM-GUI.ORG

University of Kansas

Wonpil Im

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Law●●●nce , Kansas, 66047

US

1.78●●●●1993

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University of Kansas

Sunhwan Jo

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1.17●●●●1993

su●●●●●●@gmail.com

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University of Kansas

Sunhwan Jo

2030 ●●●●●r Dr.

Law●●●nce , Kansas, 66047

US

1.17●●●●1993

su●●●●●●@gmail.com

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CHARMM-GUI | charmm-gui.org Reviews

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CHARMM is a versatile program for atomic-level simulation of. Many-particle systems, particularly macromolecules of. Biological interest. - M. Karplus. Are now available. See upload log. For update history and giving. For donation. Contact. Info is given below. CHARMM-GUI is powered by CHARMM, an academic research program used world-wide for macromolecular dynamics and mechanics ( http:/ www.charmm.org. Academic users can obtain CHARMM freely from http:/ www.charmm.org. Department of Biological Sciences.

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1 about us

2 input generator

3 archive

4 charmm docs

5 lectures

6 movie gallery

7 video demo

8 citations

9 update log

10 jobs and events

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CHARMM-GUI | charmm-gui.org Reviews

https://charmm-gui.org

CHARMM is a versatile program for atomic-level simulation of. Many-particle systems, particularly macromolecules of. Biological interest. - M. Karplus. Are now available. See upload log. For update history and giving. For donation. Contact. Info is given below. CHARMM-GUI is powered by CHARMM, an academic research program used world-wide for macromolecular dynamics and mechanics ( http:/ www.charmm.org. Academic users can obtain CHARMM freely from http:/ www.charmm.org. Department of Biological Sciences.

INTERNAL PAGES

charmm-gui.org

1

Welcome to CHARMM’s documentation! — CHARMM v35b1 documentation

http://www.charmm-gui.org/charmmdoc

CHARMM is a versatile program for atomic-level simulation of. Many-particle systems, particularly macromolecules of. Biological interest. - M. Karplus. CHARMM-GUI has updated. See our upload log. To see what is changed. Contact us ( E-mail. If you have any problem/question/comment. Model Building and Manipulation. Scalar Commands for Atom Properties. The Ewald Summation Method. Merck Molecular Force Field. Quantum and Molecular Mechanical FF. Effective Energy Function 1. The SASA implicit solvation model.

2

Welcome to CHARMM’s documentation! — CHARMM v35b1 documentation

http://www.charmm-gui.org/charmmdoc/index.html

CHARMM is a versatile program for atomic-level simulation of. Many-particle systems, particularly macromolecules of. Biological interest. - M. Karplus. CHARMM-GUI has updated. See our upload log. To see what is changed. Contact us ( E-mail. If you have any problem/question/comment. Model Building and Manipulation. Scalar Commands for Atom Properties. The Ewald Summation Method. Merck Molecular Force Field. Quantum and Molecular Mechanical FF. Effective Energy Function 1. The SASA implicit solvation model.

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cgenff.paramchem.org

Links

https://cgenff.paramchem.org/commonFiles/simulationLinks.php

More Info and Tools. Acknowledgements, Privacy and Disclaimers. The CGenFF program is a product of the discontinued ParamChem project. Check out its technology page. Where other exciting force field-related technologies are listed. The CHARMM force field. Is distributed freely and independently from the CHARMM program; both can be used with other molecular simulation codes such as NAMD, GROMACS,. Provide some additional resources pertaining to the CHARMM General Force Field (CGenFF) and program. If you t...

compbio.lehigh.edu

Publications

http://compbio.lehigh.edu/Publications/index.html

S-J Park, J. Lee, D.S. Patel, H. Ma, H.S. Lee, S. Jo, and W. Im. Glycan Reader is Improved to Recognize Most Sugar Types and Chemical Modifications in the Protein Data Bank. S Kim, J. Lee, S. Jo, C.L. Brooks III, H.S. Lee, and W. Im. CHARMM-GUI Ligand Reader and Modeler for CHARMM Force Field Generation of Small Molecules. J Lee, Z. Ren, M. Zhou, and W. Im. Molecular Simulation and Biochemical Studies Support an Elevator-Type Transport Mechanism in EIIC. DS Patel, Y. Qi, and W. Im. S Jo, X. Cheng, J&...

mackerell.umaryland.edu

MacKerell Lab

http://mackerell.umaryland.edu/forum.shtml

Force Field Development Resources. Dept of Pharmaceutical Sciences. The CHARMM forum, http:/ www.charmm.org/ubbthreads/. Offers access to questions and answers to a wide variety of CHARMM related use and other issues. Please join the forum and use it as a resource to answer your questions; please check to previously posted questions before sending yours. It will save us a lot of time! Additional sites to access CHARMM documentation and other information:. Http:/ brooks.chem.lsa.umich.edu/.

memprotein.org

In The Press | Membrane Protein Structural Dynamics Gateway

http://memprotein.org/news-and-events/in-the-press

Annual Meeting and Conference. Conformational Transitions in P-class ATPases. Structural Dynamics of ABC Transporter. The Transport Cycle in Neurotransmitter Uptake Systems. Dynamics of Ion Permeation and Conformational Coupling in – KcsA. Conformational Dynamics in the CLC Channel/Transporter Family. Structural Dynamics of Hormone-Receptor Action. Investigating Conformational Changes in a Saccharide Transporter. Conformational Dynamics of a Glutamate Transporter Homologue. Tutorial Files and Methods.

memprotein.org

News and Updates | Membrane Protein Structural Dynamics Gateway

http://memprotein.org/news-and-events/news

Annual Meeting and Conference. Conformational Transitions in P-class ATPases. Structural Dynamics of ABC Transporter. The Transport Cycle in Neurotransmitter Uptake Systems. Dynamics of Ion Permeation and Conformational Coupling in – KcsA. Conformational Dynamics in the CLC Channel/Transporter Family. Structural Dynamics of Hormone-Receptor Action. Investigating Conformational Changes in a Saccharide Transporter. Conformational Dynamics of a Glutamate Transporter Homologue. Tutorial Files and Methods.

biochem.umn.edu

Current DDT Lab Personnel

http://biochem.umn.edu/CurrentPersonnel.html

Http:/ www.umn.edu/. Go to the U of M home page. Search U of M Web sites. David D. Thomas. 5-290 Nils Hasselmo Hall. Dept of Biochemistry (BMBB). Minneapolis, MN 55455. 5-290 Nils Hasselmo Hall. Dept of Biochemistry (BMBB). Minneapolis, MN 55455. Spectroscopic Investigation of Oxidative Stress in Myosin. Assistant Scientist - Lab Manager. 5-101C Nils Hasselmo Hall. Dept of Biochemistry (BMBB). Minneapolis, MN 55455. Molecular biology (restriction digest, ligation, plasmid purification). MA Titus, and D&#...

compbio.lehigh.edu

Wonpil Im Research Group

http://compbio.lehigh.edu/index.html

Research in our group is focused on the applications of theoretical/computational methods to chemical and physical problems in biology and material science. Specific research interests are: (see the details. Protein/peptide interactions with/in biological membranes. Transmembrane-induced signaling and regulation. NMR structure calculation and refinement. Modeling and simulation of glycoconjugates ( GlycanStructure.ORG. Bacterial outer membranes and interactions with proteins. As well as ST-analyzer.

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charmm-gui.org

CHARMM-GUI

CHARMM is a versatile program for atomic-level simulation of. Many-particle systems, particularly macromolecules of. Biological interest. - M. Karplus. Are now available. See upload log. For update history and giving. For donation. Contact. Info is given below. CHARMM-GUI is powered by CHARMM, an academic research program used world-wide for macromolecular dynamics and mechanics ( http:/ www.charmm.org. Academic users can obtain CHARMM freely from http:/ www.charmm.org. Department of Biological Sciences.

charmm-tutorial.org

CHARMMing Web interface

CHARMMing (CHARMM INterface and Graphics). CHARMMing contains an integrated set of tools for uploading structures, performing simulations, and viewing the results. In order to provide the best possible user experience, it incorporates a number of freely available tools such as JSmol. For visualization and an automatic residue topology file (RTF) generator (GENRTF) which generates the necessary information for atoms and residues that are currently not supported by the CHARMM force fields. CHARMMing is cur...

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Keep me signed in. This is the web-site for the CHARMM Development Project. Developers should sign up and post their developments on the appropriate bulletine board: project descriptions to Developments. Bugs and fixes to Bugfixes. And testcases and other issues to Discussions. These will be compiled into a release notes in Releases. Keep the format guided in the "notice" post on the boards, respectively. Resources. Contains useful informations, tips, and guidelines for developers. Drude energy and force.

charmm.net

CHARMM Development Project

This is the web-site for the CHARMM Development Project. Developers should sign up and post their developments on the appropriate bulletine board: project descriptions to Developments. Bugs and fixes to Bugfixes. And testcases and other issues to Discussions. These will be compiled into a release notes in Releases. Keep the format guided in the "notice" post on the boards, respectively. Resources. Contains useful informations, tips, and guidelines for developers. C42b2 and c43a2 Releases.

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Chemistry at HARvard Macromolecular Mechanics). A molecular simulation program. With broad application to many-particle systems with a comprehensive set of energy functions, a variety of enhanced sampling methods. And support for multi-scale techniques. Including QM/MM, MM/CG, and a range of implicit solvent models. CHARMM primarily targets biological systems. CHARMM contains a comprehensive set of analysis. And model builiding tools. CHARMM achieves high performance. And can be obtained here. Jing Huang...

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