With due respect ! I want to ask that, If it is protonated at neutral pH, what about the local pka of the active site key residues involved ? would not it make any difference if it adds extra H-atom and actual case is different when the reaction is carried out ?
With Kind regards Prem On Fri, Aug 8, 2014 at 4:21 AM, Boaz Shaanan <[email protected]> wrote: > 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: > [email protected] <[email protected]> Phone: 972-8-647-2220 Skype: > boaz.shaanan Fax: 972-8-647-2992 or 972-8-646-1710 * > > > > > > ------------------------------ > *From:* CCP4 bulletin board [[email protected]] on behalf of Abhinav > Kumar [[email protected]] > *Sent:* Thursday, August 07, 2014 8:04 PM > *To:* [email protected] > *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 <[email protected]> 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 >> >> >> > >
