Hi Amali, Aspartic acid is also assumed to be charged (like Arg), but with opposite sign. Acids like Asp release hydrogens, bases like Arg accept hydrogens. That's why in one case there is one hydrogen more that what you are expecting and in the other case there is one hydrogen less. Nothing wrong with PyMOL, is just assuming the most plausible scenario (at pH 7) anyone can assume without any other information and without solving equations like the Poisson-Boltzmann equation. Almost every molecular modeling package out there is making the same assumptions.
Cheers, Osvaldo. On Wed, Nov 11, 2015 at 7:50 AM, Amali Guruge <amaligg2...@gmail.com> wrote: > Dear Prof. Osvaldo, > > Arg residue problem is solved. Thank you very much. Other thing is for > Aspartic acid the program doesn't add H to the OH > group. What is the reason behind this. > > Thank you. > > On Wed, Nov 11, 2015 at 11:17 AM, Osvaldo Martin <aloctavo...@gmail.com> > wrote: > >> 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 residue of equal sign. >> >> What is the other think you notice? >> >> Cheers, >> Osvaldo. >> PD: please just call me Osvaldo. >> >> >> On Wed, Nov 11, 2015 at 6:25 AM, Amali Guruge <amaligg2...@gmail.com> >> wrote: >> >>> Dear Prof. Osvaldo, >>> >>> When I use the command h_add, the pymol program adds H to the enzyme. >>> But when it contains Arg group it added two hydrogens to =NH group. How can >>> I solve that problem? I noticed another thing. >>> >>> Thank you in advance. >>> >>> On Mon, Nov 9, 2015 at 6:00 PM, Amali Guruge <amaligg2...@gmail.com> >>> wrote: >>> >>>> Thank you very much for the reply. >>>> >>>> On Sat, Nov 7, 2015 at 1:34 PM, Osvaldo Martin <aloctavo...@gmail.com> >>>> wrote: >>>> >>>>> Hi Amali, >>>>> >>>>> PyMOL has parameters like h_bond_max_angle that are defined in terms >>>>> of aceptor-donor-hydrogen, hence if hydrogens are not present PyMOL has to >>>>> guess the position of hydrogens. >>>>> >>>>> If you need to add hydrogens you can use PyMOL’s h_add >>>>> <http://pymolwiki.org/index.php/H_Add> command, alternatively you can >>>>> use openbabel <http://openbabel.org/wiki/Main_Page>. >>>>> >>>>> Cheers, >>>>> >>>>> Osvaldo. >>>>> >>>>> On Sat, Nov 7, 2015 at 2:33 AM, Amali Guruge <amaligg2...@gmail.com> >>>>> wrote: >>>>> >>>>> Dear All, >>>>>> >>>>>> My question is related to find the polar contacts between an enzyme >>>>>> and ligand. I want to know when we find polar contacts, >>>>>> >>>>>> 1) protein should contain H atoms or not? >>>>>> >>>>>> 2) ligand molecule should contain all H atoms or not >>>>>> >>>>>> Please can anyone help me. >>>>>> >>>>>> Thank you in advance. >>>>>> >>>>>> >>>>>> ------------------------------------------------------------------------------ >>>>>> >>>>>> _______________________________________________ >>>>>> PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) >>>>>> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users >>>>>> Archives: >>>>>> http://www.mail-archive.com/pymol-users@lists.sourceforge.net >>>>>> >>>>> >>>>> >>>> >>>> >>> >> >
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