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...

05 June 2019 961 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...

11 December 2018 4,161 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...

05 June 2018 6,824 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...

03 April 2018 5,690 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,...

10 November 2017 2,509 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...

04 May 2017 2,324 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...

04 May 2016 1,503 7 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 9,653 4 View

Enhanced Yellow Fluorescent Protein (Aequorea victoria) DNA sequence?

I am on the lookout for the Enhanced Yellow Fluorescent Protein (Aequorea victoria) DNA sequence. Does anyone know where I can find it? Thank you in advance

03 March 2021 3,568 1 View

After a reference from Int J Body Compos Res, can any body help?

Hi, I am after the reference below, my library says it cannot obtain a copy either locally or internationally, any help appreciated! Chris Wang ZM, Heshka S, Wielopolski L, Pi-Sunyer FX, Pierson...

03 March 2021 6,193 1 View

Can we block unwanted images during the x-ray prediction?

i am try to classify the x-ray images. During classification , can i block unwanted images (except x-ray image).

03 March 2021 7,100 1 View

How to repeat an operation on an atom selection for multiple times in PyMol?

Hi, I am trying to construct a multi-layer fibril structure from a single layer in PyMol by translating the layer along the fibril axis. For now, I am able to use the Translate command in PyMol...

02 March 2021 4,569 4 View

Do anyone here can help us in the field of molecular docking?

We have synthesized various metal complexes with different environment around the metals. Now to see the application of synthesized complexes we need this study also. we are also interested in...

01 March 2021 1,899 2 View

Does anyone know to clarify these changes?

01 March 2021 1,290 2 View

How to calculate the crystallinity of cellulose film?

27 February 2021 2,753 4 View

What could be the reason for not having further low chi square value (better agreement) in my refinement result?

I have tried every combination of parameter changes and after that i have a poor chi square value. I can't get it lower any further. I know there have been a lot of discussion about Rietveld...

26 February 2021 8,480 3 View

Is there a recitation score bank system for fair evaluation and assessment of student recitation?

In actual and virtual class, even if there is rubric for recitation, students may still fail to receive fair grades or scores. Others are active in recitation and others are not or others may fail...

26 February 2021 8,387 3 View

Can anyone share his experience regards Smoothing in origin?

I am working on TiO2 composite material and the results of XRD have a lot of small/junk peaks and while I apply a smooth filter in Origin then the other characteristics peaks disappear so anyone...

26 February 2021 8,183 3 View