Dear Amberist
Good evening...
I have a novel peptide and is incorporated with non standard amino acid residues. I have already cracked all the possible steps to handle it in AMBER and now I have obtained preliminary structure with the NOE violation of 0.2-0.7 A* (200 noes + 20 hydrogen bonds). But my system visually looks 70% close to the expected structure but I would like to improve it. Currently I have annealed my system with noe, hydrogen bond restraints in vacuum.
My questions are...
1) What are next steps that I should take after having a preliminary structure from SANDER (with RST) to further improve its quality. Unfortunately, my sample is not labelled and quality of 2D NOESY spectra is good but I cant play more to obtain additional restraints. I don't have RDC, I cant have Dihedral for this nonstandard part. So, could any one suggest me steps one must follow after annealing with RST in vacuum.?
2) Is it possible to perform annealing in TIP3BOX. I have tried it blowup the system. If any one have good scripts for this good I request them? I have tried in GB but my structure didn't improve. I just used the GB annealing scripts on the same vacuum prmtop, .rst files.
I would very grateful for your help, suggestions...
thanks in advanceVince
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Received on Thu Oct 22 2015 - 08:30:04 PDT
