[gmx-users] Trouble in generating gro file for GROMACS MD simulation.

RAHUL SURESH drrahulsuresh at gmail.com
Sat Mar 30 09:09:45 CET 2019

On Sat 30 Mar, 2019, 1:33 PM Aparna Chaturvedi, <
aparna.chaturvedi27 at gmail.com> 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.

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
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