I am trying to crosslink my protein by gluteraldehyde but after crosslinking multimeric form of protein is not able to run on SDS PAGE even after 6 hrs long run at 90V.
Presumably the degree of cross linking is too high and the molecule is now huge. If you are trying to immobilise a protein for absorption processes you could try linking to an inert bead like sepharose. It would help if we knew what you are trying to do and why
As Paul mentioned the crosslinking degree is too high so I would suggest either to shorten the reaction or to reduce crosslinking agent concentration (or both).
We always do titration the GA concentration with a certain time on ice, say 10 min on ice with different concentration of GA. Do not forget to quench it with Tris in the end. By this way, we find the right crosslinking conditions. It is different from case to case.