Farzane Jalalypour

6 Questions 38 Answers 0 Followers

Questions related from Farzane Jalalypour

How to calculate and change omega angle in VMD?

Dear All, I need to change the omega angle of some residues in my protein in order to flip them from trans to cis state. I tried geometry script of VMD but It calculated all Phi, Psi , and omega...

09 January 2020 6,516 4 View

Calculating Potential of mean force (PMF) using SMD trajectories!?

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26 February 2019 4,492 1 View

Compatible forcefield with charmm to simulate a protein containing Trimethyllysin!?

Hi all, I am trying to simulate a protein containing a modified Lysin : Trimethyllysine. I am a NAMD user and I couldn't find a proper forcefield (topology and parameter files) with charmm yet....

03 December 2018 4,828 8 View

How should I define "non protein" parts of PDB in Parameter file(charmm)?

Hi, I need help with performing a simulation of a ligand and a protein. I am using psfgen code and add a ligand as the second segment but my parameter file couldnt recognize the new molecule...

21 September 2018 2,881 5 View

What is the best alghorithm to superpose two protein? Same in sequence vary in shape?

these two algorithms seems fast and efficient for aligning (superpose) two proteins: Acta Chrystallogr. Sect. A 61 (2005) 478 [doi: 10.1107/S0108767305015266] J. Comput. Chem. 31 (2010)...

19 September 2018 2,235 1 View

Temperature control (via langevin) in Steered Molecular Dynamics!?

Dear all, I would like to know about the temperature control in Steered Molecular Dynamics. should I turn off langevin control in steered molecular dynamic? Thank you

06 June 2018 10,057 3 View