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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