[sassie-web/sassie2-feedback][suggestion] 'TAMC no accepted model' xin.gao.15@ucl.ac.uk

[genapp.not...@gmail.com]

subject : TAMC no accepted model
from : xingaoucl
email : xin.g...@ucl.ac.uk
level : suggestion
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Dear Joseph: Hope you are doing well. I did a test this this TAMC run but got no accepted model.I am not sure is this the problem of pdb file or psf file. Hope you can give me some suggestions. Many Thanks

[mads...@gmail.com]

Hi.

I am looking at your system.  It looks, at first glance, like an antibody but the segment/segname distribution is non-canonical.  In the screen shot below I have colored the segnames using different colors and the glycans are VDW space filling models.  Usually the glycans are bonded to the Fc region, which if I assume is the case here then the Fc should only include two heavy chain segments and the Fab regions should be roughly 1/2 heavy chain and 1/2 light chain.  But as they are colored by segname what I assume are Fab consist of only a single segname (see picture below).

That doesn’t mean that your arrangement will not work in TAMC.  That said, you still have all protein segnames as chain P and both glycans as chain C.  

Given your structure (PDB/PSF) have you energy minimized the model using SASSIE (or independently)?

Cheers,

Joseph