Hi,
I am willing to calculate the MMPBSA contribution of one peptide to a unit cell consisting of about 30 copies of the same peptide. They are found very well ordered on the unit cell, and I guess I want to keep them more or less like that through the whole simulation. My goal is to calculate the DG energy of the interaction between one peptide (ligand) and the other 29 (receptor). the complex is simply all of them. So the DG will estimate the contribution of one peptide to the Unit Cell. It’s important to mention that one peptide interacts with another 3 or four, so I need to use the full Unit Cell. My question is somehat trivial but I am unsure what is the best way to proceed:
I thought to make MD production with weak restraints (restraint_wt=0.5 ?) on the backbone of all the peptide for about 50 ns, and allow free movement of all other atoms. Does it sounds like a good approach?
In this way I will keep more or less the unit cell conformation (otherwise they just start to move around), which we suppose is stable also in solution since they are amphipathic and the crystal shows a very nice hydrophobic core between peptides. Will that provide a good estimation of DG through the MMPBSA methodology?
Another suggestions?
Thanks a lot,
Fabian
____________________
Dr. Fabian Glaser
Head of the Structural Bioinformatics section
Bioinformatics Knowledge Unit - BKU
The Lorry I. Lokey Interdisciplinary Center for Life Sciences and Engineering
Technion - Israel Institute of Technology, Haifa 32000, ISRAEL
fglaser at technion dot ac dot il
Tel: +972 4 8293701
http://bku.technion.ac.il <
http://bku.technion.ac.il/>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Thu Oct 22 2015 - 06:30:06 PDT
