Dear users, I would like to change the orientation of an hydrogen of a D-serine (my ligand) and of a serine (as protein residue). How is it possible by using Gromacs 5.0.4? Thank you
First: how did you get the current orientation of hydrogen atoms? Did you use any software that optimzes hydrogen bond network or just adds H atoms randomly? Gromacs' pdb2gmx usually does here a good job.
In general changing the orientation of hydrogen atoms means simply changing coordinates of these atom in a PDB file. These can be easily done by hand (eiditing the PDB file in text mode)or using many of the available visualizers (pymol, Maestro). However, if you're preparing the structure to run MD that is not tha crucial, since during the MD run they will change the orientations anyhow.
Thank you for your advice. Does someone know how to do that in Pymol?
You may have a look at the following link:
http://www.pymolwiki.org/index.php/Modeling_and_Editing_Structures
Or you can do that without command line.
On the right panel you should see "Mouse Mode" which is usually set to "3-Button Editing". Click it to change to "3-Buttin Editing" (or 2-Button) to edit the structure. Ctrl+left button allows you to move single atoms as long as you have "Selection Mode -> Atoms" chosen from the "Mouse" panel.
I suggest you to use the RTFM* method.
* RTFM = "read the fucking manual...."
- Badges
- Science topic