Hi! We have a problem with a protein-ligand-protein simulation. It is a somewhat large system (approx. 360 amino acid residues with approx. 70 monosaccharides), that requires a larger box for proper simulation. We used exclusions (especifically for the problematic atoms) and restrictions (tested values of 5000, 2000, 1000 - for backbone and for monosaccharides), both combined and individually, and when they were kept for the entire simulation, it went just fine. But when these restrictions and exclusions were removed, the glycan portion, that isnt connected to any of the proteins explodes. Any suggestions?
Thank you in advance, Giovana Bergamini Faculdade de Farmácia Grupo de Bioinformatica Estrutural Universidade Federal do Rio Grande do Sul Av. Bento Gonçalves, 9500 Prédio 43431, sala 202 CEP 91500-970, CP 15005, Porto Alegre, RS, Brazil tel.: +55 51 3308 7770 http://www.cbiot. ufrgs.br/ bioinfo -------------------------------------------------------------------- Centro de Biotecnologia da Universidade Federal do Rio Grande do Sul -- gmx-users mailing list [email protected] http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! 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
