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#30472 - 08/01/12 03:50 PM CHARMM36 additive force field release
alex Offline

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Registered: 10/04/03
Posts: 780
Hello,

This post announces the availability of a new release of the new CHARMM toppar files. These include the new C36 additive protein, nucleic acid, lipid, and carbohydrate releases as well as the CGenFF files as of July 2012. The toppar files are now in a new format that allows them to be read individually such that different parts of the force field (eg. proteins and nucleic acids) can be accessed without creating toppar files that contain both the protein and nucleic acid parameters. Note that this includes a toppar stream file for water and ions that must be explicitly read as water and the ions are no longer included in the biomolecular or CGenFF toppar files. See 00toppar_file_format.txt, included in the .tgz file, for details including an example on how to read the files into CHARMM.

have fun, alex

The gzipped tar file, toppar_c36_jul12.tgz toppar_c36_aug12.tgz, containing the files may be accessed at

http://mackerell.umaryland.edu/CHARMM_ff_params.html

Reference for the new CHARMM36 protein FF.

Robert B. Best, R.B., Xiao Zhu, X., Shim, J., Lopes, P.,Mittal, J., Feig, M. and MacKerell, A.D., Jr. Optimization of the additive CHARMM all-atom protein force field targeting improved sampling of the backbone phi, psi and sidechain chi1 and chi2 dihedral angles. Journal of Chemical Theory and Computation, In press, DOI: 10.1021/ct300400x

Remaining references in the respective toppar files.



Edited by rmv (03/08/13 04:16 PM)
Edit Reason: revised file name

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#30919 - 11/15/12 07:54 PM Re: CHARMM36 additive force field release [Re: alex]
Kenno Offline
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Registered: 12/19/05
Posts: 1535
Loc: Baltimore, MD
In the meanwhile, it has been printed. Just to make it as easy as possible to find the paper, here's the full citation:
Robert B. Best, Xiao Zhu, Jihyun Shim, Pedro E. M. Lopes, Jeetain Mittal, Michael Feig and Alexander D. MacKerell, Jr. Optimization of the Additive CHARMM All-Atom Protein Force Field Targeting Improved Sampling of the Backbone φ, ψ and Side-Chain χ1 and χ2 Dihedral Angles. Journal of Chemical Theory and Computation 2012, 8(9), 3257-3273.

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#31771 - 04/16/13 11:57 AM Re: CHARMM36 additive force field release [Re: alex]
rmv Online   content

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Additional information on the C36 lipid parameters can be found here
_________________________
Rick Venable
computational chemist


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#32370 - 08/07/13 01:07 PM Re: CHARMM36 additive force field release [Re: rmv]
rmv Online   content

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Registered: 09/17/03
Posts: 8373
Loc: 39 03 48 N, 77 06 54 W
New NBFIX terms for Na+ (SOD) interactions with oxygen atom types that have large negative partial charges (carboxylate, phosphate, ester) have been developed for use with lipids and have now been accepted for publication. The values and additional details are in this post.
_________________________
Rick Venable
computational chemist


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#34360 - 09/01/14 06:48 PM Re: CHARMM36 additive force field release [Re: alex]
alex Offline

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Registered: 10/04/03
Posts: 780
An update of the CHARMM36 force field (toppar_c36_aug14.tgz is now available on http://mackerell.umaryland.edu/charmm_ff.shtml. Note that there have been NO changes to the biomolecular FF, only minor corrections and additions as described below.

Also, the polarizable Drude2013 force field is now available on http://mackerell.umaryland.edu/charmm_ff.shtml. It is also available on the CHARMM-Gui; see the Drude Prepper module.

alex


1) Minor bug fixes

2) CHARMM36 FFs in Gromacs format ( http://mackerell.umaryland.edu/charmm_ff.shtml#gromacs )

3) Addition of various water models in non_charmm subdirectory

4) stream files moved to subdirectories ( toppar/stream/*/*.str )

5) Addition of a collection of lipids and glycolipids in the stream/lipid subdirectory

6) Addition of glycoprotein linkages in stream/prot subdirectory

7) Release of polarizable classical Drude-2013 oscililator model for proteins, DNA,
DPPC lipids and carbohydrates (polyols and hexapyranoses).

8) Patches for ionized cysteine and serine added to protein parent files

9) Addition of posttranslation patches in stream/prot subdirectory
_________________________
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University of Maryland
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