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GLYCAM-Web / gmml

Glycam Molecular Modeling Library
GNU Lesser General Public License v3.0
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Anomer-Anomer bug for DNeup5Aca (and others) #156

Closed gitoliver closed 5 months ago

gitoliver commented 1 year ago

This doesn't work: DGalpNAca1-2DNeup5Aca Because it sees a 2SA and we don't have a prep file for that. Ok. However: This does produce a default structure and off file: DNeup5Aca2-1DGalpNAca because it's finding the 0SA and 1VA prep files. Note that energy minimization isn't happening when I build this via glycam actual, but gmml thinks everything is ok. But that is a separate issue, order shouldn't matter for these ano-ano linkages. I should be able to write: DNeup5Aca2-1DGalpNAca DGalpNAca1-2DNeup5Aca And after automatic ordering in gmml get the exact same structure every time regardless.

gitoliver commented 1 year ago

More notes: gmml-test is throwing the unexpected throw type, my feature branch is more correctly throwing: Prep entry not found for 2SB or 2SA

gitoliver commented 5 months ago

Now we can build this sequence either way.

Another bug (that I'll open is) We don't have parameters for the dihedrals and this is causing other problems. programs/amber/bin/teLeap: Warning! The unperturbed charge of the unit (123456788.000000) is not zero.

/programs/amber/bin/teLeap: Warning! Close contact of 1.372056 angstroms between .R<2SA 1>.A<O2 1> and .R<2SA 1>.A<HHH 39>

/programs/amber/bin/teLeap: Warning! Close contact of 1.410400 angstroms between .R<2SA 1>.A<O6 28> and .R<2SA 1>.A<HHH 39> Checking parameters for unit 'CONDENSEDSEQUENCE'. Checking for bond parameters.

/programs/amber/bin/teLeap: Error! Could not find bond parameter for: Cy -
Checking for angle parameters.

/programs/amber/bin/teLeap: Error! Could not find angle parameter: Os - Cy -

/programs/amber/bin/teLeap: Error! Could not find angle parameter: C - Cy -

/programs/amber/bin/teLeap: Error! Could not find angle parameter: Cg - Cy -

/programs/amber/bin/teLeap: Error! Could not find angle parameter: Oy - Cy -

/programs/amber/bin/teLeap: Warning! There are missing parameters. check: Warnings: 4

So tleap fails, but gems or the website isn't handling that properly.