I don't know if the morpholine should be protonated at not, but if you think it should, you can edit C:\Users\---\AppData\Roaming\OpenBabel-2.3.2\data\phmodel.txt as you like. One way to do this is to copy it to your current directory, edit it and run obabel from the command-line there. We would welcome any improvements to the model.
- Noel On 13 August 2013 20:51, Bennion, Brian <benni...@llnl.gov> wrote: > Hello, > > While trying to prepare a ligand for further calculations I find that one > that contains a morpholine substituent is not protonated properly. At > physiological pH I would expect the nitrogen on the morpholine to be > protonated. Is this incorrect? > The coordinates are given below for the heavy atoms. > > The aliphatic nitrogen seems to be protonated properly. > > Thank you. > Brian > > ATOM 3529 C5 TIM A 401 3.037 1.145 51.139 1.00 45.16 C > ATOM 3530 C6 TIM A 401 3.227 1.181 52.657 1.00 57.05 C > ATOM 3531 O1 TIM A 401 2.525 0.109 53.257 1.00 58.33 O > ATOM 3532 C2 TIM A 401 1.125 0.224 53.044 1.00 53.51 C > ATOM 3533 C3 TIM A 401 0.710 0.379 51.570 1.00 51.17 C > ATOM 3534 N4 TIM A 401 1.640 1.118 50.754 1.00 50.77 N > ATOM 3535 C7 TIM A 401 1.306 1.594 49.509 1.00 53.55 C > ATOM 3536 N8 TIM A 401 0.645 0.822 48.631 1.00 58.54 N > ATOM 3537 S9 TIM A 401 0.376 1.667 47.251 1.00 55.87 S > ATOM 3538 N10 TIM A 401 1.084 3.083 47.666 1.00 49.53 N > ATOM 3539 C11 TIM A 401 1.554 2.967 48.898 1.00 52.80 C > ATOM 3540 O12 TIM A 401 2.233 3.973 49.543 1.00 52.38 O > ATOM 3541 C13 TIM A 401 2.227 5.300 48.941 1.00 43.69 C > ATOM 3542 C14 TIM A 401 3.213 6.032 49.863 1.00 42.67 C > ATOM 3543 O15 TIM A 401 3.888 7.083 49.235 1.00 42.10 O > ATOM 3544 C16 TIM A 401 2.480 6.515 51.102 1.00 44.11 C > ATOM 3545 N17 TIM A 401 3.043 7.593 51.881 1.00 48.54 N > ATOM 3546 C18 TIM A 401 2.542 7.436 53.270 1.00 41.41 C > ATOM 3547 C19 TIM A 401 2.600 8.757 54.024 1.00 44.38 C > ATOM 3548 C20 TIM A 401 1.067 6.963 53.216 1.00 36.66 C > ATOM 3549 C21 TIM A 401 3.404 6.393 54.011 1.00 46.82 C > > ------------------------------------------------------------------------------ > Get 100% visibility into Java/.NET code with AppDynamics Lite! > It's a free troubleshooting tool designed for production. > Get down to code-level detail for bottlenecks, with <2% overhead. > Download for free and get started troubleshooting in minutes. > http://pubads.g.doubleclick.net/gampad/clk?id=48897031&iu=/4140/ostg.clktrk > _______________________________________________ > OpenBabel-discuss mailing list > OpenBabel-discuss@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/openbabel-discuss ------------------------------------------------------------------------------ Introducing Performance Central, a new site from SourceForge and AppDynamics. Performance Central is your source for news, insights, analysis and resources for efficient Application Performance Management. Visit us today! http://pubads.g.doubleclick.net/gampad/clk?id=48897511&iu=/4140/ostg.clktrk _______________________________________________ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
