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
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
wrote:
> Hi Amali,
>
> By the =NH group do you mean on
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
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.
--
__
What I've done before is to draw a line between two pseudo-atoms placed
at the center of each ring.
HTH,
Matthew Baumgartner
On 11/10/2015 02:08 AM, Albert wrote:
I think the major concern is how Pymol depicts the pi-pi stacking
Of course we can identify such interaction immediately as soo
