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
gromacs.
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!
See:
http://lists.gromacs.org/pipermail/gmx-users/2011-April/060108.html
which is codified in the tables of
https://uab.hyperfine.info/trac/molsim/wiki/gromacs Charmm FF Conversion
information.
--
==
Peter C. Lai| University of Alabama-Birmingham
Programmer/Analyst | KAUL 752A
Genetics, Div. of Research | 705 South 20th Street
p...@uab.edu| Birmingham AL 35294-4461
(205) 690-0808 |
==
--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
