Tini Chu

10 Questions 22 Answers 0 Followers

Questions related from Tini Chu

How to parameterize the new ligand of a complex in AMBER?

Dear all, I am currently working on the simulation study of a complex whose ligand cannot be automatically parameterized. I have been using AMBER to do the parameterization, and now I have...

03 February 2023 318 2 View

How to replace a specific fragment on PyMol or Chimera?

Dear all, I am searching for methods to replace the fragment. I have a model and a fragment of this protein from experiment. I would like to replace the corresponding part on the model(green) with...

02 June 2022 4,307 4 View

(solved) Why is my molecule (after 100ns md simulations) flipping in VMD?

Dear all, Sorry for not being able to describe my question properly in the title. I just finished 100 ns simulation with GROMACS for my molecule, and I visualized the trajectory in VMD. The input...

01 March 2022 4,081 6 View

How to model terminal missing residues in Chimera?

Dear all, I was trying to fix the missing residues for my PDB structure, but I couldn't use all atom option to let Chimera go through the entire sequence. It turns out with an error message. I...

13 January 2022 5,085 3 View

AutoDock Tool error: AttributeError: Bond instance has no attribute 'activeTors' how to fix?

Dear all, I just tried to prepare my receptor for docking with ADT, and it returns error message. However, I did the same thing with same protein(chains A-F) and everything were good. This time I...

11 November 2021 6,299 9 View

How to really get started with molecular simulation?

Dear all, I have started to study molecular simulation for weeks, and have studied the basic theory of molecular simulation from lectures and videos. I am currently trying to do some hands-on...

25 October 2021 5,022 8 View

Why does my downloaded PDB file have one more identical chain?

Dear all, I wonder why I can only see one chain on PDB website and see 2 identical chains in PDB file that I downloaded(opened with PyMol). I checked the sequence as well as ligands/ ions...

01 January 1970 4,687 7 View

Is it necessary adjust protonation states to make the protein and ligand have same pKa(pH) before simulating the complex?

Dear all, I wonder if it's a necessary case to adjust the protonation state before conducting simulations. To illustrate the question clearly, here is my case: I just used H++ to predict pH values...

01 January 1970 5,901 3 View

In which case should we remove restraints of the system during equilibration in molecular simulation?

Dear all, I have been confused about the use of restraints in the molecular simulation. As far as I understand, the restraints are added in energy minimization so that only the solvent will...

01 January 1970 1,155 5 View

Are the types of o-linked glycans on one specific glycoprotein all the same?

Dear all, I have been trying to build glycans computationally by myself, and this question just came to my mind. Suppose this glycoprotein has both O-linked and N-linked glycosylation, and we...

01 January 1970 9,617 4 View