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#27972 - 07/21/11 09:26 AM how to calculate partial charge for ligand?
albumns Offline
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Registered: 10/08/07
Posts: 46
Hello:

I've got a nonstandard residue -CHO in the N-term of a peptide. I would like to calculate the partial charge of this group based on CHARMM FF method because the whole system protein coupled with derived peptide would be submitted to MD simulation under CHARMM 36 FF.

Thank you very much.

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#27977 - 07/21/11 11:26 AM Re: how to calculate partial charge for ligand? [Re: albumns]
Ken Offline
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Registered: 02/03/06
Posts: 22
Loc: New Hampshire
Since you have posted this to the Accelrys forum my guess is that by "CHARMM FF method" you refer to the "CHARMm FF" (AKA "Momany-Rone"). This was created by Accelrys, whereas "charmm27, "charmm36", etc. generally refer to the academic set of force fields. Mixing them would be ill advised.
If your goal is to run your final simulations using "CHARMM 36 ff" presumably top_all36_carb and par_all36_carb along with the most recent protein FF then I would not recommend using partial charges for the nonstandard residues based on CHARMm FF (Momany-Rone). Discovery studio can indeed auto-generate residue topologies and charges, and parameter records for a variety of force fields, but nothing more recent than charmm 27 at present. Therefore, if you wish to use charmm36 and have non-standard residues you might obtain charges and other parameters using QM calculations. There is a wealth of information on this topic in Dr. MacKerrell's website: http://mackerell.umaryland.edu/Empirical_FF_Dev.html
_________________________
Ken Butenhof, Ph. D.
Principal Scientist
Accelrys, Inc.

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#27981 - 07/21/11 12:38 PM Re: how to calculate partial charge for ligand? [Re: Ken]
rmv Online   content

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Registered: 09/17/03
Posts: 8079
Loc: 39 03 48 N, 77 06 54 W
The academic lipid force field has also been updated to a c36 version.

The Parameter forum here has a lot of information about extending the academic force field in a variety of ways.
_________________________
Rick Venable
computational chemist


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#33315 - 01/20/14 03:10 PM Re: how to calculate partial charge for ligand? [Re: albumns]
Ken Offline
Forum Member

Registered: 02/03/06
Posts: 22
Loc: New Hampshire
Discover Studio can be used to set up and analyze the results of CHARMm calculations. As noted above it supports a variety of forcefields including charmm36 FF parameters (as of DS 4.0), for example those generated by Paramchem for non-standard residues.
_________________________
Ken Butenhof, Ph. D.
Principal Scientist
Accelrys, Inc.

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