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Compatibility of Charmm22 Parameters in Charmm36
#38189 02/03/21 08:05 PM
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akash Offline OP
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Hello,

I have a molecule which was parametrized using the Charmm 22 force field. I want to make some modifications to the molecule (add side chain groups) and use the Charmm36 forcefield for that. Essentially, I will have a molecule in which half of the atom types would in charmm36 format, and the other half would be in charmm22.

Are charmm22 parameters compatible in the charmm36 forcefield. If yes, how is the interfacing done? I just want to ensure if I can proceed with atomtypes/parameters from 2 different versions of charmm.

Please let me know if I should provide more information to clarify my doubt. Thank you.

Kind Regards,
Akash

Re: Compatibility of Charmm22 Parameters in Charmm36
akash #38191 02/03/21 10:38 PM
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rmv Online Content
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The parameters from those two versions are not compatible, there have been too many changes in values and names.

I recommend using the CGenFF site as the first step in C36 compatible parameters for the whole molecule.


Rick Venable
computational chemist

Re: Compatibility of Charmm22 Parameters in Charmm36
rmv #38192 02/04/21 10:52 PM
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akash Offline OP
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Thank you so much for your help. I am trying to use the findings of piece of work that was entirely parameterized using the CHARMM22 forcefield. Sprcifcially, the authors parameterize a specific biomolecule's backbone dihedrals. CGENFF gives me a new set of atomtypes/paramters. How do I incorporate the previously derived dihedral parameters into the input files generated by CGENFF? Do I use the CGENFF atomtypes along with the previously derived dihedral parameters (harmonic constant, multiplicity, etc)?

Re: Compatibility of Charmm22 Parameters in Charmm36
akash #38193 02/05/21 12:08 AM
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Do not do anything until you evaluate the two force fields for the same molecule. To create a new molecule, you should not mix values from two different parameter sets in ad hoc way w/o extensive testing of the result.

Using the original unmodified molecule, I would run two sets of low friction (collision freq. = 1) vacuum Langevin MD with a dielectric constant of 80., something like ten replicas with each FF for quite a few ns. Then I would use all the replicas for each FF to get p(phi) for each dihedral and compare them graphically, probably as a PMF.

If this molecule is important to your work, then it is critical to proceed carefully, esp. when adding new molecules to well established force field.


Rick Venable
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Re: Compatibility of Charmm22 Parameters in Charmm36
rmv #38194 02/05/21 12:58 AM
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akash Offline OP
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Thank you so much for a detailed description. This is extremely helpful. I would like to have your inputs in one more thing: is there a specific reason I need to do Vacuum Langevin MD simulations. What is the difference if I do regular MD with a single molecule in water? Would the solvent affect our assessment of the dihedral distributions/PMF plots?

Thank you again for your help and advice.

Kind Regards,
Akash

Re: Compatibility of Charmm22 Parameters in Charmm36
akash #38195 02/05/21 03:43 PM
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You can do the simulations in water, it will just take longer to get results. If you have the time and resources, you could do both.


Rick Venable
computational chemist

Re: Compatibility of Charmm22 Parameters in Charmm36
akash #38196 02/05/21 06:54 PM
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akash Offline OP
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That makes sense. I will carry out the simulations as per your advice.

Thank you so much for your help.

Kind Regards,
Akash


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