14 Questions 16 Answers 0 Followers
Questions related from Maryam Bakhtiari
Hey Guys, I am calculationg radius of gyration for 1ubq. My reference file is a pdb file. and I cannot change it. So I have to deal with it!! The problem is that I receive 2 warnings: WARNING:...
12 December 2017 5,241 6 View
Hey Guys, I have a ubiquitin, I am planning to claculate radius of gyration for residue 1 to 24 and 25 to 76. How can I make this? What command shall I use? Thank you. Maryam
12 December 2017 3,445 3 View
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...
11 November 2017 6,058 1 View
Dear friends, I have a problem with gromacs. My protein rotates in md simulations. I run the simulation in 300K but the protein rotates and suddenly starts doing weird things! It completely...
10 October 2017 1,626 7 View
Hello! How can I calculate radius of gyration for the proteins using .gro files. We use .tpr and .xtc files to calculate R of G but right now I need to use my .gro files. Thank you.
08 August 2017 3,117 4 View
Hello friends! I have 100 .gro files. How can I combine them and create just one .gro file? Thank you! Maryam
08 August 2017 8,811 1 View
Hello friends, I am really really desparate right now! I am working in negative mode in Mass spec. I added formic acid+acetonitrile+water to my protein and I didn't receive any signal. I added...
03 March 2017 3,796 10 View
Hello Friends, I look for a paper/book/website to study about the relationship among salt bridges / proteins/genetics and evolution. I have searched alot but I failed. Can you please advise me? Best,
02 February 2017 9,626 3 View
Hello everyone! I have 1 central protein in pymol with 6 surrounding proteins. I want to find a command to say: please select nterm only on central protein. How can I do this? Thank you.
02 February 2017 1,050 0 View
Hi! How can I select only 1 atom in pymol? only 1 atom, instead of selecting residues. Thanks
02 February 2017 5,738 1 View
Suppose that I have measured distances between positive and negative sides and all of the proteins are in cartoon format. Now, I want to hide the whole proteins except the charged chains. I mean,...
02 February 2017 9,216 9 View
Hello Friends, I need some books about salt bridges. DO you know some?! Thanks
01 January 1970 7,409 0 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...
01 January 1970 4,803 3 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 1,065 2 View
