Hello
i have a protein that is made up of three different parts: extracellular, transmembrane, intracellular. i want to simulate molecular dynamics. i connected the end atoms of these parts with VMD, and then i saved the pdb file, but when i make the psf file, the parts of the protein are not connected and are separete. i do not know where the problem is???
please help me :((
thanks
How did you connect the parts? Can you share the "before" and "after" structures?
If you have the separate structures in a pdb file, you can join them with modeller and then with the joined structure, you can create the psf file in VMD.
Psf gen works or command lines:
https://www.ks.uiuc.edu/Training/Tutorials/namd/namd-tutorial-html/node6.html
Ramin Ekhteiari Salmas Further explanation about the structure I have. I am designing a car t cell, that I designed the extracellular part by myself through phage display and the intermembrane and intracellular part is composed of CD28 and CD3zeta. Now I want to connect the end of the extracellular sequence to the beginning of the intermembrane sequence and the end of the intermembrane sequence to the beginning of the intracellular sequence. I make the connection with vmd, but I have a problem making psf, and after making psf, the different parts of my structure are not connected. For simulation I need my structures to be connected.
Alejandro Soto-Ospina No, I can not use the modeller, because the transmembrane part is not modelled and I have to model each part of my structure separately.
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