search

PodewitzLab / PyConSolv

GNU General Public License v3.0
19 stars 3 forks source link

Error is writing LIG.mol2 file during MCPB step. #55

Closed tanoury1 closed 9 months ago

tanoury1 commented 9 months ago

Hi again Radu, With the system I am studying (2-aminopyridine reaction with N2O3 in water), there seems to be an error in the LIG.mol2 file that is written during the mcpb step. The file, attached, is trying to form a bond between atoms 27 and 30, but there are only 21 atoms in the LIG system. The error is in the tleap.log file. I've also attached the Orca optimized structure (to save you the time of running the initial QM optimization). In my system, the charges are: 2-aminopyridine: 0 NO2: -1 NO: +1

I get the error with versions 1.0.4 and 1.0.5. LIG.mol2.txt orca_opt.xyz.txt tleap.log.txt

Jerry

Lapsis-glitch commented 9 months ago

Hi Jerry,

I will have a look at the issue today and try to fix it.

Thanks, Radu

Lapsis-glitch commented 9 months ago

Hi Jerry, The fix for this is now live in 1.0.6

Best, Radu

tanoury1 commented 9 months ago

Awesome. I’ll give it a try today.

On Fri, Jan 26, 2024 at 11:32 AM Lapsis-glitch @.***> wrote:

Hi Jerry, The fix for this is now live in 1.0.6

Best, Radu

— Reply to this email directly, view it on GitHub https://github.com/PodewitzLab/PyConSolv/issues/55#issuecomment-1912346650, or unsubscribe https://github.com/notifications/unsubscribe-auth/AOA2OYQA6F3TRN5ZTWEDBODYQPLCVAVCNFSM6AAAAABCFBEFHGVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTSMJSGM2DMNRVGA . You are receiving this because you authored the thread.Message ID: @.***>

Lapsis-glitch commented 9 months ago

Hi Jerry, I will close this issue if it's resolved for you as well.

Best, Radu

tanoury1 commented 9 months ago

Yes it is.

On Tue, Jan 30, 2024 at 5:12 AM Lapsis-glitch @.***> wrote:

Hi Jerry, I will close this issue if it's resolved for you as well.

Best, Radu

— Reply to this email directly, view it on GitHub https://github.com/PodewitzLab/PyConSolv/issues/55#issuecomment-1916504977, or unsubscribe https://github.com/notifications/unsubscribe-auth/AOA2OYTXJ772HT4GTOEG5F3YRDBRLAVCNFSM6AAAAABCFBEFHGVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTSMJWGUYDIOJXG4 . You are receiving this because you authored the thread.Message ID: @.***>

Lapsis-glitch commented 9 months ago

Issue resolved with merge #56