[gmx-users] FE+3 simulation

Shumaila Khan shumailakhan432 at yahoo.com
Wed Feb 1 13:06:16 CET 2017

Hello,        I am new to gromacs. I want to simulate heme of hemoglobin.I am using Gromacs version 5.0.7. and force feild  GROMOS 96 43a1 and spc water model.I built Heme topology on Prodrg and Swiss Param but after 1ns analysis, Fe and OXY are missing. I have given Fe in prodrg but they responded Prodrg contains limited atoms like C,H, Be etc and they dont have topology for Fe. Kindly tell me appropriate force feild which I shoud use and How to generate iron and oxygen topology? or any alternative which I should use.

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