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]
<mailto:[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 <tel:%28650%29%20926-2992>
