So, I currently working on a chimeric receptor originate from EnvZ and HB-EGF receptor protein. I have already made the 3D structure of this chimeric. Then, I want predict the orientation of this chimeric on membrane. I already used TOPSCONS and TMHMM for prediction, and it goes well. Now, i want to construct it in a 3D structure in PyMOL.
Try the ProBLM webserver (http://compbio.clemson.edu/sapp/problm_webserver/) to insert the model of your receptor into the membrane. You can then visualize the resulting pdb file in PyMOL.
Annemarie Honegger thank you so much for your answer. I really appreciate it.
I already try ProBLM, but I can not run this webserver because there is an issue. Do you have any other webserver recommendation?
Thankyou
I think there is a PlugIn for VMD which generates membrane for membrane protein molecular dynamics: https://www.ks.uiuc.edu/Research/vmd/plugins/membrane/
You can also try CHARMM-GUI to build your system and generate the MD inputs for a number of different softwares.
http://www.charmm-gui.org/?doc=input/membrane
Yes, thankyou Pedro Túlio Resende-Lara for your help. But, unfortunately, both CHARMM-GUI and proBLM webservers didn't work in my country. So I think i need another alternative. Thankyou in advance
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