Amir Zeb

9 Questions 13 Answers 0 Followers

Questions related from Amir Zeb

How to optimize geometry of nanoparticle for docking?

Hello Folks, I want to dock nano-particle like Fe2O3 in protein. I need to optimize the geometry of such nano-particle structure. Is there any online approach to assign partial charge and...

01 January 2018 6,394 6 View

How to explain the WHATCHECK out put of SAVES Validation server?

Hello everyone,Previously, i asked a question regarding SAVES validation server (https://services.mbi.ucla.edu/SAVES/),I want to extend that question again. I could not understand why the output...

06 June 2017 5,537 0 View

How to elaborate SAVES Server output results?

Hello Folks,I need the basic explanatory document of SAVES server https://services.mbi.ucla.edu/SAVES/ that can explain how the results are calculated?Let me code an example here:The WHATCHEK...

05 May 2017 3,448 0 View

What's the difference between the I-TASSER and LOMETS?

Hello dear members, I want to build homology model for my target protein while using online server where the algorithm should be based on threading, because the available templates from PDB for my...

02 February 2017 1,648 2 View

Should i restraint protein and ligand in md production?

Hello folks, I want to conduct md simulation to explore the comparative stability and interaction mechanism of the reference compound (experimentally determined) and the newly screened candidate...

02 February 2017 9,271 4 View

How to ensure that whether the charge groups assigned to atoms in itp file are correct or not?

Hello, I have generated itp file for the ligand via SwissParam because I'm using CHARMm ff. I want to confirm that whether the charge groups assigned to each atom of the ligand are either correct...

11 November 2016 2,506 0 View

Is there any hard and fast range for NVT and NPT to decide whether our system is equilibrated or not?

Hello, I prepared my protein-ligand complex for MD run, the average value for NVT is 299.99 which looks pretty satisfactory, but for NPT, the average value is 10.01 which is strange to me. I...

11 November 2016 2,415 7 View

What's the basic criteria to select a suitable forcefield for protein-ligand complex MD simulation in gromacs?

Hello, I want to simulate my protein-lignad complex, but there is no forcefield information cited yet for this specific protein. I'm seeking the basic criteria which is taking in consideration to...

11 November 2016 948 9 View

Hello, How may we merge the .itp files contents when we using Amber force field in gromacs?

Hello, I have generated ligand's topology files through acpype, the number of ligands are two. when we want to run simulation on gromacs, we gonna merging the two files especially their atomtype...

10 October 2016 4,831 0 View