Avogadro2 can not properly read MOPAC aux file

[Miroslav_Ilias]

Hello,

With MOPAC, I run small peptide, 1IYT.

However, Avogadro2 does not read properly MOPAC’s aux file, instead of all 630 atoms it reads in only a small subset.

1IYT_geopt_pm7water.tar (576 KB)

Any help,please ?

[ghutchis]

It looks like the MOPAC parsing code didn’t imagine so many coordinates:

 ATOM_X:ANGSTROMS[01890]=

I’m not sure why MOPAC starts this with 0 but the code assumed that it would go to, e.g. 9999 instead of 09999.

So the current code reads 189 coordinates = 63 atoms only.

I can submit a fix after lecture tonight.

[ghutchis]

Okay, here’s the patch:

Fix import of large (>1000 atom) MOPAC aux files

I’ll merge later tonight, at which point it will be available in the continuous releases:

Release continuous · OpenChemistry/avogadrolibs

[Miroslav_Ilias]

@ghutchis

s the patch:

Thanks. When it will be ready in Windows nigthly build please ?

[ghutchis]

We switched to recommending the continuous builds because you can see the timestamp. We’re never quite sure about the nightly.

If you install the current continuous, it should have the fix.

[Miroslav_Ilias]

SOLVED with the fresh continuous Avogadro2 MS Windows build.

Fine now, reading MOPAC aux file of such big molecule works, see