Large molecule has final charge

[BJWiley233]

Hey Brandon,

I was running poltype for 90 atom molecule and the esp from Psi4 keep getting killed with the basis used in poltype, so need to use less memory and used the 6-311G(d) basis set. My final molecule after running analyze had -0.43844 charge. I tarred up the folder attached. It also has negative charge on the combined.xyz of -0.00007 Electrons but not on the original tinker 408956424.xyz file. https://drive.google.com/file/d/13lahKVNAjrJ-wd6aa-nW0qYPdWPKCjIN/view?usp=sharing

$ analyze final.xyz -k final.key em | grep -A11 Charge
 Total Electric Charge :                  0.43844 Electrons

 Dipole Moment Magnitude :              17370.525 Debye

$ analyze 408956424.xyz -k 408956424.key em | grep -A11 Charge
 Total Electric Charge :                  0.00000 Electrons

 Dipole Moment Magnitude :                  5.629 Debye

[BJWiley233]

Also is there a good way to look at the CSV files from the final simulations in Excel? The Greek letters look wonky for me.

[lukeanewman]

@BJWiley233 I am having a similar issue. I constructed the parameters for a large molecule that should be neutral but instead has a -0.1 charge when the Poltype parameters are all put together. Have you figured out where your charge was originating from?

[pren]

Does every atom have multiples assigned. Use "analyze" with ep option.

Thanks, Pengyu

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From: lukeanewman @.***> Sent: Tuesday, August 22, 2023 12:10 PM To: TinkerTools/poltype2 Cc: Subscribed Subject: Re: [TinkerTools/poltype2] Large molecule has final charge (Issue #21)

@BJWiley233https://github.com/BJWiley233 I am having a similar issue. I constructed the parameters for a large molecule that should be neutral but instead has a -0.1 charge when the Poltype parameters are all put together. Have you figured out where your charge was originating from?

— Reply to this email directly, view it on GitHubhttps://github.com/TinkerTools/poltype2/issues/21#issuecomment-1688601462, or unsubscribehttps://github.com/notifications/unsubscribe-auth/ABNC6XSG6247AHGHV6OGVBLXWTRYBANCNFSM6AAAAAATMST7SE. You are receiving this because you are subscribed to this thread.Message ID: @.***>

[lukeanewman]

Yes, analyze/minimize/dynamic do not complain about missing parameters. I ran smaller molecule fragments on poltype and combined the parameters manually because the molecule was large and the fragmenter protocol was not working. I believe the partial charge is a result of my manual combination but I can not figure out a way to pinpoint my error.