Mohd Athar

9 Questions 66 Answers 0 Followers

Questions related from Mohd Athar

Modification in the input files for depicting surface (weak) ligand binding ?

Hi, we are trying to simulate ligand which is binding to the surface (exposed cavity) of a protein. The ligand topology was created from the antechamber and the complex was simulated using...

06 June 2019 1,076 2 View

Why the polynomial equation (including quadratic equation) is not so popular in QSAR modeling?

Studies have shown that quadratic equation gives improved correlation coefficents than linear equation. Still, Linear correlation is more popular amung the modeling community. What are the...

12 December 2018 4,273 3 View

Is the cpu load and processor affect the molecular dynamics simulations results?

If I simulate the two similar systems with similar parameters under different CPU load and nodes/processors. Then, will I get the replicate results ? I am asking this to be ensure as I am going...

06 June 2018 6,938 4 View

How to give the pseudopotential for complex having two metal with zero and +2 charge in Gaussian?

I am trying to optimize a inorganic complex having Ag (0) and Fe(II) states (overall charge is +2). For that i am using Lanl2dz ecp with the given additional input 2 1 C...

04 April 2018 5,829 2 View

Is there any visualisation software that can display detailed protein-protein interactions?

I have docked two protein in order to comprehend the residue involve in PPI interaction. Now, I want to visualise detailed interaction types and bonding pattern. I have tried Discovery studio,...

11 November 2017 2,629 7 View

Modelling of ionic supramolecular complexes ?

I am interested in studying the dynamic behavior via MD simulations by utilizing the benchmarked OPLS force field. In this course, I have fired various calculation with QM optimized structure...

05 May 2017 2,427 2 View

How to give the input for oxidation state of the metal in Gaussian?

while optimizing host-guest complex in GAUSSIAN at any level, we have the option of only mentioning overall charge on the system not on a particular atom. In such case, if I want to represent the...

05 May 2016 1,635 7 View

X-ray coordinates of pdb

where to find the X-ray coordinates of a particular protein deposited in RCSB Protein Data Bank (PDB).

09 September 2015 9,369 1 View

Molecular Dynamics simulation of a protein (2FOM) with larger RMSD fluctutation ?

Hello Everybody ! I am trying to perform MD simulation of a protease apoprotein (pdbid: 2FOM) as well as its complex with inhibitor. Upon analyzing, I found that there are huge fluctuations in...

01 January 1970 9,752 4 View