elbow, how to get partial charges in mol2 output file?
Dear phenixbbers, The partial charges are not written in mol2 output files generated by elbow. Is there any way to change that behavior? Probably by editing tripos_mol2_writer.py? Thanks for helping. Florian -- La chance ne sourit qu'aux esprits bien préparés. Louis Pasteur
Florian
You need to actually calculate the partial charges. Currently that can only
be done by using the --opt flag to run the RM1/AM1 semi-empirical QM
method. Add this flag to your eLBOW job and the partial charges will be
included in the output files.
Cheers
Nigel
On Tue, Aug 5, 2014 at 8:05 AM, Florian Nachon
-- Nigel W. Moriarty Building 64R0246B, Physical Biosciences Division Lawrence Berkeley National Laboratory Berkeley, CA 94720-8235 Phone : 510-486-5709 Email : NWMoriarty@LBL.gov Fax : 510-486-5909 Web : CCI.LBL.gov
On 5 août 2014, at 18:15, Nigel Moriarty
Florian
You need to actually calculate the partial charges. Currently that can only be done by using the --opt flag to run the RM1/AM1 semi-empirical QM method. Add this flag to your eLBOW job and the partial charges will be included in the output files.
Nigel In my configuration, partial charges were surprisingly not present despite the --opt flag. But, I was using PHENIX version dev-1539. Apparently, this bug was solved sometimes in between this earlier version and the last nightly :) You helped me to figure out that this behavior was not normal, thank you :) Cheers! Florian -- La chance ne sourit qu'aux esprits bien préparés. Louis Pasteur
On 5 août 2014, at 19:48, Florian Nachon
And for information, the bug is also present in the latest official 1.9 release (version 1692). Florian -- La chance ne sourit qu'aux esprits bien préparés. Louis Pasteur
participants (2)
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Florian Nachon -
Nigel Moriarty