Hi Amali,
For adding hydrogens, I have found that PyMOL does an OK job normally,
but if you need more accurate placement of hydrogens, I can recommend
using Reduce.
http://kinemage.biochem.duke.edu/software/reduce.php
HTH,
Matthew Baumgartner
On 11/11/2015 02:06 AM, Osvaldo Martin wrote:
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
<mailto: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 <mailto: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 <mailto: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 <mailto: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 <mailto: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
<mailto: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
<mailto: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
------------------------------------------------------------------------------
_______________________________________________
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
------------------------------------------------------------------------------
_______________________________________________
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
