[gmx-users] how to use charmm ff in gmx and carbohydrate forcefield
Peter C. Lai
pcl at uab.edu
Thu Mar 1 00:50:59 CET 2012
On 2012-02-29 05:11:48PM -0600, Tom wrote:
> Dear Gromacs User and developers:
> Please help with 2 questions:
> 1) Does the converted charmm forcefield (charmm36 or 27) in gromacs
> include forcefield parameters for carbohydrate (sugar)? I looked
> through *itp and can not find them in converted charmm36 and 27 in
The only sugars that ship with the conversions are the ribose variants
found in dna and rna. You can extract those and rebalance the charges,
but if you want something more exotic then you'll probably have to
do the conversions from charmm36/xx
> 2) How to convert charmm forcefield parameters and use in gromacs?
> To save time to look through gromacs source code, any expert can give
> some guidances?
> My question is beside the difference in the unit, like kcal, A
> (charmm) vs. kj, nm (gromacs),
> do i need to care about any conversion of the potential format?
> For example: i have a set of nonbonded and bonded parameters with the
> original charmm
> formate and want to use in gromacs, do i need to convert anything,
> because of the format difference in the potential formula, such as
> potential of vdw, bond, angle, dihedral angle, and improper dihedral
> angle before i add them to *itp and *rtp file?
> Thanks a lot for the information!
which is codified in the tables of
https://uab.hyperfine.info/trac/molsim/wiki/gromacs Charmm FF Conversion
Peter C. Lai | University of Alabama-Birmingham
Programmer/Analyst | KAUL 752A
Genetics, Div. of Research | 705 South 20th Street
pcl at uab.edu | Birmingham AL 35294-4461
(205) 690-0808 |
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