RES: [gmx-users] covalent linkage with protein

Elias Ramos de Souza eramos at
Thu Aug 10 02:00:02 CEST 2006

Dear gromacs users,
We have a similar problem as we need to covalently link Fe atoms from a
iron-sulfur cluster  with S atoms from cys residues. We have already
good parameters for iron and for inorganic sulfur. However we don't know
how to covalently bound Fe atoms to organic S atoms. Could anybody give
us some help?
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

-----Mensagem original-----
De: gmx-users-bounces at [mailto:gmx-users-bounces at]
Em nome de mprabha at
Enviada em: Wednesday, August 09, 2006 9:51 AM
Para: gmx-users at
Assunto: [gmx-users] covalent linkage with protein

Dear users

I have a peg chain (I created the topology using PRODRG)
and I run independent chain using Gromacs. I want to covalently link the
(5000k) peg chain with cys residue. How can we accomplish this.

for glycosylation I usually modify the residue and create a
new residue type. earlier gromacs does not allow any covalent linkage
between two systems
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