On Sat 30 Mar, 2019, 1:33 PM Aparna Chaturvedi, < [email protected]> wrote:
> Hi, > I tried to generate a .gro file for my MD simulation job, but since my > protein contains a metal in it's active sites, the .gro file could not > be generated. The error says, the metal is not defined in database and > suggested to edit the residue.dat file. How can I edit this file to > define my metal. > Hi Specify the metal atom parameters in gromacs folder. Include LJ parameters, (refer articles) of the metal atom in the necessary files ie in ffnonbonded ffbonded atmtype rtp and whereevrr necessary. Please refer papers of Dr Subramanian boobathy and PK kolandaivel. Please, reply soon. > > Regards, > Aparna Chaturvedi > -- > 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 [email protected]. > -- 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 [email protected].
