[gmx-users] Help in parametrisation

onetwo twoone21 at rediffmail.com
Wed Jun 23 17:08:30 CEST 2010

Hello All,

I am new in this field, and I want to do simulation study on one of the protein conatining a metal ion and study its ability to form co-oridnation bond with other ligand, which is not defined in GROMOS force field which I have tried. If this choice of force field is correct for such type of study ?

I have read Gromacs Manual Chapter 5, also I am following this gromacs mailing list for quite some time to get a help on how to include a new metal ion or a new ligand in their simulation and they have been refered to refer to the  http://www.gromacs.org/Documentation/How-tos/Parameterization,

but in this its not mentioned that how to actually do parameterization

neither in manual it has been told on how to generate it ( due apologies,,I know, I may be wrong )

and it is more difficult for a person like me who doesnt have much knowledge in this field, so if someone can please help me guiding how to do parameterisation, I know this is not a trivial task, but still help in this regard may help many other fellow users besides me.
Thanks in advance
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