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 <[EMAIL PROTECTED]> 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: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] Em nome de [EMAIL PROTECTED] Enviada em: Wednesday, August 09, 2006 9:51 AM Para: [email protected] 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 _______________________________________________ gmx-users mailing list [email protected] http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php _______________________________________________ gmx-users mailing list [email protected] http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
-- 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 _______________________________________________ gmx-users mailing list [email protected] http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
