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Questions related from Maryam Bakhtiari
Hey guys, There is a strange thing that is going on with my laptop. I receive messages like: ssh is not recognized as an internal or external command but I know I have installed both SSH client...
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Hi friends! I am running my simulations in negative ion mode, gromacs. The problem is that, my proteins completely unfold, and rotate badly. At the very begininng they start unfolding and...
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Hi friends! Does heme group in Cytc and myoglobin have residues? Is heme a residue by itself? I looked at .pdb file and I found the order of atoms but still I have problems finding out what heme...
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Hi Friends, I was wondering if you know how to generate only and only 6 moleculaes around one molecule in Pymol. I do this: Action--> Generate --> symmetry mates --> 6a but 12 molecuales...
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Hello Friends, I have a question about pymol an I was wondering if you could advise me. How can see salt bridges of a protein in Pymol?!
29 January 2017 487 10 View
Hey guys, Can someone please, explain what is the point of doing equilibration, for the proteins, in the "vacuum" in GROMACS? I know it is needed for the solution phase because one must...
01 January 1970 2,259 2 View
Hello friends, I have a question. In pymol, when we measure the distance between 2 group which form a salt bridge, to which atoms should we pay attention? The distance between carbon in COO- and...
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