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.