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: [email protected] [[email protected]] On Behalf Of sonali dhindwal [[email protected]] 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 -- gmx-users mailing list [email protected] http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [email protected]. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
