Read the papers for the forcefield, that will tell you how things are parameterised.
On Sat, 15 Sep. 2018, 2:49 am RAHUL SURESH, <drrahulsur...@gmail.com> wrote: > Hi Users > > I am performing a simulation for a bonded metal-protein complex system. > Here I am aware of adding the essential parameters in ffbonded .itp. The > force constant value (kb) in the ffbonded.itp file is calculated using > Gaussian. I would like to clarify the method I have adopted to measure kb > value. > > Here the metal is bonded with three residues of a protein. I have isolated > the metal-bonded residue and optimized using gaussian calculated the Kb > value. Now in ffbonded.itp file, I have added Metal and residue atom bond > length and Kb value obtained from QM results, just like > CU O 0.20134 507545. > > likewise, I have added all the bonds but kb remain the same. > > Regarding bond angle and dihedral, if the metal is bonded with oxygen of > two histidines, what should be the nomenclature in naming atoms. Naming can > be our choice or does it need to follow any protocol? > > How to calculate the cth value for the bond angle? > > How do we determine the coefficients of dihedral? > > Do I make the procedure complicated or can anyone suggest if any better > methods? > > Sorry I have dumped the mail with too many questions. > > -- > *Regards,* > *Rahul * > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.