[gmx-users] Fe - Cys S bonds

[eramos at cefetba.br]

Hi all,

I am simulating a metalloprotein with two 4Fe-4S cluster. In the pdb file
Fe atoms are covalently bonded to Cys-S atoms. However, after minimization
the Fe – Cys S bonds atoms are broken and new bonds Fe-Fe inside the
cluster are formed. Is it possible to impose that bonds Fe – Cys S atoms
are not broken both in energy minimization and in md run?

Thank you in advance,



Elias Ramos de Souza

Grupo de Pesquisa em Biofísica Teórica e Computacional

Departamento de Ciências Aplicadas

Centro Federal de Educação Tecnológica da Bahia