Im using molecular dynamics to study stabilization of protein at low pH but when am checking by VMD it shows no any salt bridges also I was used different software like gromacs salt bridges but also no result .can any suggestions for this problem ?
Why would you expect salt bridges at low pH? Depending on the definition of "low," you likely have some (all?) acid groups protonated, which means they won't form salt bridges with positively charged groups like Lys and Arg. They may form hydrogen bonds, but they'll probably be weak.
Why would you expect salt bridges at low pH? Depending on the definition of "low," you likely have some (all?) acid groups protonated, which means they won't form salt bridges with positively charged groups like Lys and Arg. They may form hydrogen bonds, but they'll probably be weak.
(1) The salt bridge is detected or calculated if two oppositely charged group is closely located. Therefore, as Lemkul had mentioned , little salt bridge will detected if you had protonated ASP and GLU .
(2) If you had intended the protonation of histidine, you can check whether you had properly selected the protonated conformation during preparation of the protein structure. For example, if you had used gmx2pdb with '-his' flags, there will be HISH residue in the topology file if you used GROMOS force field (HIP for AMBER force field).
Dear Ibrahim,
A salt bridge is mainly a coulombic energy interaction between the charges of two or more groups, which depends on pH, the geometry and the distance between the interacting charges. Low pH influences in the protonation state of residues (Dr. Lemkul answer). I think you have to check these issues in your structure and topolgy file.
For the visualisation of salt bridges you can use the features of the “Salt Bridges” Plugin for VMD (attached you can find the link), throught you can define cutoffs and distances.
Miguel
http://www.ks.uiuc.edu/Research/vmd/plugins/saltbr/
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