[gmx-users] atom types @ bonded parameters

David van der Spoel spoel at xray.bmc.uu.se
Fri May 18 17:52:13 CEST 2007

Francesco Pietra wrote:
> Thanks.
> The molecules have no repetitive units, though they
> have recurring moieties, such as five-membered to
> nine-membered saturated heterocycles, variously
> substituted. Is it safe to carry out the frequency
> task on each type of recurring moiety? I understand
> that without seeing it is difficult to judge, though
> my concept should be clear: evaluating the bonded
> parameters from sections of the actual molecule.
yes, this is how all biomolecular force fields are made. you might want 
to check up structure databases, there probably are crystal structures 
for the compounds.

your biggest problem will be the nonbonded parameters however...
you probably want to check out recent papers from the amber and/or opls 
people. you may also want to look up the antechamber program which 
generates force fields for arbitrary  (well, almost) molecules.

> With my molecules of 90 to 450 atoms, a QM geometry
> optimization/frequence calculation would be too time
> consuming at DFT theory, if a reliable functional and
> basis set is choose.

> Thanks
> francesco 

David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se

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