[gmx-users] covalent linkage with protein

[Tsjerk Wassenaar]

Hi Elias, Prabharakan.

In order to achieve this you have to manually merge two partial
topologies. In the case of PEG and a protein, assuming that both
topologies are present, the topologies have to be physically merged
into a single topology, renumbering all atoms (mind bonds, angles,
etc) of the second part of the topology. Following, one has to add a
number of bonded terms, pairs and possibly exclusions for the
interactions between the two parts. IIRC Anton Feenstra has
(submitted) a tool to renumber topologies after merging, which would
make life a bit easier.

I could imagine that it would be good having a tool or a slight
modification of the topology parsing routines to allow simple merging
of partial topologies, such that the topologies of A and B are
combined using a simple section with descriptions of the interactions
between the systems based on the original atom numbers of both
subsystems. This could also solve recurrent problems concerning the
application of distance_restraints between different chains. But that
is for the developers or someone else to add...

Hope it helps,

Tsjerk

On 8/10/06, Elias Ramos de Souza <eramos at cefetba.br> wrote:
> 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
>
> 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 gromacs.org [mailto:gmx-users-bounces at gromacs.org]
> Em nome de mprabha at fiu.edu
> Enviada em: Wednesday, August 09, 2006 9:51 AM
> Para: gmx-users at gromacs.org
> 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.
> prabhakaran
>
> PS
> 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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-- 

Tsjerk A. Wassenaar, M.Sc.
Groningen Biomolecular Sciences and Biotechnology Institute (GBB)
Dept. of Biophysical Chemistry
University of Groningen
Nijenborgh 4
9747AG Groningen, The Netherlands
+31 50 363 4336