Hi Elias, Unless you're doing QMMM calculations, it is out of the question that bonds are broken and formed during your simulation. Whether atoms are bonded depends merely on the definitions in the topology file. The bonds you see in a structure visualization program are usually inferred from distances and therefore you can conclude that some atoms which are bonded get away from each other, despite the bonds, while atoms which are not bonded appear to give strong interactions, bringing them at too short distances (displaying as bonds).
To cut it short, you have a problem in your topology. Also, an iron cluster will be problematic in terms of the parameters. Where did you get your parameters or how did you derive them? Tsjerk On 7/29/06, [EMAIL PROTECTED] <[EMAIL PROTECTED]> wrote:
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 _______________________________________________ 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
