Question about atomic charges on bio-molecule?

How to assign atomic charges on bio-molecules which were built by a Glycam Carbohydrate builder? The (.pdb) files generated by carbo-builder are without charges of the atom,? Any help would be...

03 December 2020 8,964 1 View

How to determine liquid film thickness (experimentally and theoretically), if the film is floating on another immiscible liquid?

I would like to determine the thickness of a liquid film floating (uniformly/non-uniformly) on another immiscible liquid. How to photograph the cross section of the film (in a non-invasive manner)...

03 November 2020 5,514 3 View

Is antigen retrieval step required for frozen spinal cord sections in IHC ?

I am doing co-immunostain using frozen spinal cord sections for IHC. Is it required to perform the antigen retrieval step prior to the blocking step ?

20 August 2020 4,144 0 View

After resubmitting the corrected version of my manuscript, why does it is showing as "Editor Assigned" for more than 2 months?

Based on learned reviewers given comments and suggestions I have made corrections of my manuscript and resubmit the updated version. In this stage why does it is showing as "Editor Assigned" for...

25 July 2020 5,162 3 View

Steered Molecular Dynamics Simulation using AMBER?

Hi all, I am performing steered molecular dynamics simulation of two polymer chains parallel to each other. Then, one chain has pulled using constant velocity and the trajectory I got is...

23 July 2020 7,805 2 View

Which one is floxed? What are the other methods to confirm it?

I have to collect mice embryos for my research and genotype them for KO gene. In PCR, the floxed band is always blur compare to control (control DNA from adult mice) (please see the attached...

02 June 2020 4,234 3 View

Why does the handling editor asked for major revision?

i. Although the suggested correction was very less raised by the 2 reviewers in their 2nd revision, why does the editor asked for major revision? ii. Why does the editor has given me clues to...

01 June 2020 711 12 View

Could anybody help regarding MD simulation using AMBER?

Hi All, I have build the model of cellulose polymer using xleap and hemicellulose polymer using glycam carbohydrate builder. Now, I need to place the two polymer chain parallel two each other....

20 May 2020 9,416 1 View

Is it possible to extract a particular feature from an image based on colour as a shape file using python?

I have a georeferenced image . Is it possible to extract a particular feature like drainage or roads from the geotiff based on its colour and save it as a shapefile using python?

16 March 2020 6,582 1 View

How to identify similar patterns in drainage shapefile using python?

I have a drainage/ river shapefile. If i identify a particular pattern/ feature in the drainage file then using it as input is it possible to identify similar features in the rest of the drainage...

29 January 2020 9,526 3 View

In Molecular Dynamics Simulation, how do I make changes to the force field according to my protein?

Hi In Molecular Dynamics Simulation, how do I make changes to the force field according to my protein? I got this error in the add-ion stage: Fatal error "./ amber99sb-ildn-HHH.ff / force...

01 March 2021 8,747 4 View

What is Flat Lens Antenna?

28 February 2021 5,433 3 View

Why does the sum of reaction forces not match the force component of a Free Body Cut in Abaqus?

I am using Abaqus to simulate a plate with in-plane loading. The boundary conditions allow the right edge to move up and down, the displacements on the left edge are fixed. There is no rotation...

23 February 2021 711 3 View

How to include additional force field in GROMACS?

I have a cellulose model system that is best described by the GLYCAM06 force field according to the literature. However, the set of force fields included in the GROMACS package doesn't include the...

20 February 2021 3,309 3 View

I want to simulate a system containing protein and heavy metals; which force field is most reliable for this purpose?

The protein I want to simulate has multiple heavy metals. I wanted to know which force-field I should use with GROMACS to achieve this. Most importantly, do the latest updates in the force-field...

16 February 2021 2,420 1 View

How to obtain parameters to run a simulation for benzene using CHARMM forcefield in GROMACS?

I have been reading this paper Soft Matter, 2017, 13, 1904 and in this paper, they simulate benzene in GROMACS using CHARMM. They mention that they performed simulations of benzene using the...

15 February 2021 5,561 3 View

Gromacs force field and water model recommended for protein hydrophobic study?

Dear All, I received a comment from reviewer about asking me selection of force field and water model. I choose OPLS-AAL and 3-point water model. They mentioned the combination of OPLS-AAL and SPC...

13 February 2021 1,364 3 View

Can anyone please suggest where I can find a reference for ReaxFF parameters for PTFE(Teflon) suitable for use in LAMMPS?

Trying to simulate a ice-PTFE interaction and am unable to find a reference which actually lists out forcefield parameters for PTFE-PTFE interactions using ReaxFF or even other force fields like...

08 February 2021 9,373 2 View

Distribution of modes fields ?

Hi, We find a specific distribution of electric fields in structure for different frequencies which can be seen using em solvers and known as modes. I would like to know how we can choose the...

04 February 2021 10,043 3 View

Anyone use GROMACS' pdb2gmx for Adenosine monophosphate (AMP) to use with CHARMM force field?

I am trying to use the following command in GROMACS to generate a CHARMM topology file: gmx pdb2gmx -ff charmm27 -f amp.pdb -o amp.gro -p amp.top The atom list in my pdb file (amp.pdb)...

01 February 2021 7,769 6 View