Re: [ccp4bb] Jligand help

[Boaz Shaanan]

Hi, A trick that has worked for me a few times is to skip the regularization stage in Jligand, although some may argue that it's "illegal". If your ligand/cofactor has a decent geometry without regularization it may well work for you too.      Cheers,                Boaz     Boaz Shaanan, Ph.D.                                         Dept. of Life Sciences                                      Ben-Gurion University of the Negev                          Beer-Sheva 84105                                            Israel                                                                                                                  E-mail: bshaa...@bgu.ac.il Phone: 972-8-647-2220  Skype: boaz.shaanan                  Fax:   972-8-647-2992 or 972-8-646-1710                          From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Abhinav Kumar [abhin...@slac.stanford.edu] Sent: Thursday, August 07, 2014 8:04 PM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Jligand help Thanks Ian. Is it possible to force Jligand to keep only two hydrogens in this case? I tried setting the N's charge to 0, but it reverts back to 1 after regularization. Thanks, Abhinav ______________________________________ Abhinav Kumar, Ph.D. The Joint Center for Structural Genomics MS99, SLAC National Accelerator Laboratory 2575 Sand Hill Rd, Menlo Park, CA 94025 (650) 926-2992 On 08/07/2014 10:02 AM, Ian Tickle wrote: Hi, I would say three: aliphatic amines such as the one you show are weak bases so at neutral pH the protonated form predominates.  Aromatic amines are obviously trickier. Cheers -- Ian On 7 August 2014 17:37, Abhinav Kumar <abhin...@slac.stanford.edu> wrote: Hi, I am making a ligand in Jligand (figure attached) and have a question about valency of nitrogen. Jligand puts three hydrogens on nitrogen N1 when the ligand is regularized. Should there be two hydrogens or three? -- Thanks, Abhinav ______________________________________ Abhinav Kumar, Ph.D. The Joint Center for Structural Genomics MS99, SLAC National Accelerator Laboratory 2575 Sand Hill Rd, Menlo Park, CA 94025 (650) 926-2992