Hi Amali, By the =NH group do you mean one of the nitrogens of the guanidine group? If that's the case PyMOL is doing the right thing. By default PyMOL assumes that (Arg, Lys, Glu, Asp) are charged. In general that's a reasonable assumption (if residues are exposed to the solvent or relative close to other charges of the opposite sign). Is not a good assumption if you have Arg too close to others Arg, Lys or other residues/charges of equal sign.
Cheers, Osvaldo. On Wed, Nov 11, 2015 at 6:43 AM, Amali Guruge <[email protected]> wrote: > Dear All, > > I used the command h_add to add H to the enzyme. But when it contains Arg > group it added two hydrogens to =NH group. How can I solve that problem? > > Thank you in advance. > > > ------------------------------------------------------------------------------ > > _______________________________________________ > PyMOL-users mailing list ([email protected]) > Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users > Archives: http://www.mail-archive.com/[email protected] >
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