And at what time point does it explode? What minimization, equilibration steps did you use? <br><br><div class="gmail_quote">On 13 May 2010 18:53, Giovana Bergamini <span dir="ltr"><<a href="mailto:gioberga@cbiot.ufrgs.br">gioberga@cbiot.ufrgs.br</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;"><br>
Hi!<br>
We have a problem with a protein-ligand-protein simulation. It is a somewhat<br>
large system (approx. 360 amino acid residues with approx. 70 monosaccharides),<br>
that requires a larger box for proper simulation.<br>
We used exclusions (especifically for the problematic atoms) and restrictions<br>
(tested values of 5000, 2000, 1000 - for backbone and for monosaccharides),<br>
both combined and individually, and when they were kept for the entire<br>
simulation, it went just fine. But when these restrictions and exclusions were<br>
removed, the glycan portion, that isn’t connected to any of the proteins<br>
“explodes”.<br>
Any suggestions?<br>
<br>
Thank you in advance,<br>
<br>
Giovana Bergamini<br>
Faculdade de Farmácia<br>
Grupo de Bioinformatica Estrutural<br>
Universidade Federal do Rio Grande do Sul<br>
Av. Bento Gonçalves, 9500<br>
Prédio 43431, sala 202<br>
CEP 91500-970, CP 15005, Porto Alegre, RS, Brazil<br>
tel.: +55 51 3308 7770<br>
<a href="http://www.cbiot" target="_blank">http://www.cbiot</a>. <a href="http://ufrgs.br/" target="_blank">ufrgs.br/</a> bioinfo<br>
<br>
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