[gmx-users] FES and FE molecule topology

[Kukol, Andreas]

Including Fe2+ should not be very difficult, look at the definitions for Cu2+ or others in ffG53a6.nb or any other forcefield you want to use. You need to find the correct Lennard-Jones parameters C6 and C12 and then validate your model.

I am not sure, what the FES molecule is, but developing a topology for molecules is more difficult than for single atoms. Have a look at the Gromacs help section:

http://www.gromacs.org/Documentation/How-tos/Parameterization

Best wishes
Andreas

________________________________________
From: gmx-users-bounces at gromacs.org [gmx-users-bounces at gromacs.org] On Behalf Of sonali dhindwal [sonali11dhindwal at yahoo.co.in]
Sent: 05 June 2010 14:31
To: Discussion list for GROMACS users
Subject: [gmx-users] FES and FE molecule topology

Hello All,
Could some one please help me in introducing Fe2+ and FES molecule in protein for simulation studies.
But before starting it, I am not able to generate topology file for the same.
I have tried to use HICUP database and used CNS topology file. but it is still not working.
Please help
Thanks and regards
--
Sonali Dhindwal