I have some peptides and want to see how many hydrogen bonds each could form.
Please recommend software or web sever I can use, Thank you very much!
you can freely download Discovery Studio Viewer or pymol, they have the option for calculating H-bonds and vander wall interactions.
Try VMD. It is pretty powerful software that is also free for academic/personal use and has an excellent hydrogen-bond analysis option. You can set the geometrical criteria that you wish to use for hydrogen bond definition, and if you are running a simulation it will calculate the h-bond distribution.
the answer you get will depend a bit on what else is actually around in the context of your molecule and the details of the problem you are trying to solve. Water and/or other peptides will compete differently (and in fact dynamically) for the available H bond donor/acceptor sites along your chain of interest. so, depending the level of sophistication you are going for, this rapidly becomes a research project. the level of theory needed to quantitatively assess the various competing Hbond "docking" (vs. hydration) patterns may require higher-end tools such as Gaussian or Spartan to arrive at the correct predictions. if your interest is more qualitative and/or focused on self-interactions of the peptide in an anhydrous environment, then the freeware and/or other molecular mechanics or semiempirical (which are both very fast) computational packages such as the ones mentioned above should do it.
I wrote a program to track down the hydrogen bonds between a ligand (ideally .mol2 format) and PDB. It can be accessed free through http://www.ub.edu/cbdd/?q=content/define-contacts-and-binding-site-between-given-ligand-x-ray-or-docking-and-pdb-file
You can easily modify to only work or loop every protein atoms
I hope could be useful
actually in my simulation i want to determine the hydrogen bond strength...can i calculate it? i did docking on autodock then done simulation on namd
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