I have a structure in PDB format and i know where is beta turn is forming. The structure is predicted and the residue in beta turn are not making any hydrogen bond. I am creating the structure from diheral angle using the amber and also performing the simulation using amber. I don't know how to make a hydrogen bond between two residues. Please guide me.
Thankx
If you want to see the hydrogen bonds visually, you can use VMD to open the pdb file. And you need to search how to use VMD to present the hbond on the Internet. It's hard to say in a few words. But it's not tricky, just follow the tutorial. You may change the angle and distance of the hbond to show the hbonds.
Or you can send me the PDB file. And I can make a visualization file. You can use the file to see the hbond.
The hydrogen bond is not present there, i know using prediction that beta turn is forming at a specific location. I wanted to manually make the hydrogen between two residues. I am predicting the structure from its sequence and want to make hydrogen bond between two residues.
You may have to alter the distance/angle corresponding to the atoms which you want to make H-bonds by altering their coordinates. Obviously after that you have to minimize (may be in several steps, like first with restrain then without restrain on the atoms forming H-bonds) the structure to avoid any bad contacts.
You can use Pymol for this purpose:
http://www.pymolwiki.org/index.php/Modeling_and_Editing_Structures
Hi harinder singh,
You can use "UCSF Chimera" software to add Hydrogen to your structure and also you can add hydrogen bonds to the specific residues , ligands and etc.
It is a freeware, you can download it from the link attached below.
All the best.
http://www.cgl.ucsf.edu/chimera/download.html
download and install chimera on your PC from websites earlier mentioned by udhaya kumar.
UCSF Chimera 1.10 is a best software for 3D structure editing. first u can open a coordinate file of macromolecules, if u want to add hydrogen atom. In chimera select Tools option from menu bar. then select structure editing option and select AddH OPTION.
then select method of hydrogen addition ie. steric/consider H-bonds and select protonation state for specified amino acids.
then u can inspect visually the added hydrogens is in 3D structure.
If you use the Yasara graphics package (recommended!) just use the commands 'addhyd' or 'clean'. This will add all hydrogens. If you want to make a hydrogen bond between two ("heavy") atoms, use the 'add' menu.
Dear Dr. Mahadev Asaram Jadhav,
If there are hydrogens that are misplaced in the structure after using "addh", how is that corrected?
Dear Dr. Maria,
After addition of H atom in 3D structure, till you are doubtful about its placement. you can confirm its correct placement/misplace with the method ALL-ATOM CONTACT. The tool based on this method is available on http://molprobity.biochem.duke.edu.
please use it and find out misplacement of hydrogen atom in 3D structure. if it is found in remove it.
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