Gyration for a specific part of a protein?

Hey Guys, I have a ubiquitin, I am planning to claculate radius of gyration for residue 1 to 24 and 25 to 76. How can I make this? What command shall I use? Thank you. Maryam

11 December 2017 3,373 3 View

Warning message in gromacs for radius of gyration?

Hey Guys, I am calculationg radius of gyration for 1ubq. My reference file is a pdb file. and I cannot change it. So I have to deal with it!! The problem is that I receive 2 warnings: WARNING:...

11 December 2017 5,153 6 View

Unfolding in negative ion mode in gromacs?

Hi friends! I am running my simulations in negative ion mode, gromacs. The problem is that, my proteins completely unfold, and rotate badly. At the very begininng they start unfolding and...

10 November 2017 5,988 1 View

Unwanted rotation in gromacs?

09 October 2017 1,566 7 View

How to calculate radius of gyration using .gro files?

Hello! How can I calculate radius of gyration for the proteins using .gro files. We use .tpr and .xtc files to calculate R of G but right now I need to use my .gro files. Thank you.

07 August 2017 3,062 4 View

Combining100 .gro files to just one .gro file?

Hello friends! I have 100 .gro files. How can I combine them and create just one .gro file? Thank you! Maryam

07 August 2017 8,750 1 View

Buffer or additive for Mass spec in negative ion mode?

Hello friends, I am really really desparate right now! I am working in negative mode in Mass spec. I added formic acid+acetonitrile+water to my protein and I didn't receive any signal. I added...

02 March 2017 3,735 10 View

Paper or book about the relationship among salt bridge, protein, genetics and evolution?

Hello Friends, I look for a paper/book/website to study about the relationship among salt bridges / proteins/genetics and evolution. I have searched alot but I failed. Can you please advise me? Best,

01 February 2017 9,581 3 View

How to determine nterm only on central protein?

Hello everyone! I have 1 central protein in pymol with 6 surrounding proteins. I want to find a command to say: please select nterm only on central protein. How can I do this? Thank you.

01 February 2017 996 0 View

How to select only 1 atom in pymol?

Hi! How can I select only 1 atom in pymol? only 1 atom, instead of selecting residues. Thanks

01 February 2017 5,677 1 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

Resistor definition in Piezoelectric bimorph with ANSYS workbench

Hello, good day! I am trying to simulate similar bimorph piezoelectric harvester with below commands. However, the output power doesn't change with resistor value. Please help to find the reason. ET,10,CIRCU94,0 !SET UP RESISTOR R,1,100000 !RESISTANCE VALUE TYPE,10 !SET ELEMENT TYPE E,1,2 !CREATE RESISTOR BETWEEN NODES 1 AND 2 Thanks in advance Regards,

02 March 2021 0 0 View

How to define tie constraint between rigid body and another part in dynamic explicit model of Abaqus?

Hi dear researchers I connected a rigid body into the part of my structure by tie constraint and then I added displacement to rigid body, in static general step every thing is fine and these two...

28 February 2021 3,442 2 View

What's the concentration recommend for recombinant protein use in western blotting?

I'm currently working having problem with the concentration for recombinant protein use in western blot, the one been used is Recombinant Human CD19 Fc Chimera Protein-rndsystem which does not...

24 February 2021 8,514 3 View

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22 February 2021 9,932 11 View

Is there a method for evaluating nanoparticle adhesion to epithelial tissue in vitro?

I want to measure how well nanoparticles can transfect cells based on NP adhesion properties. In the literature I find people do it in animal studies, and epithelial adhesion helps in transfection...

21 February 2021 7,791 3 View

How to select therorical or conceptual framework for any proposed qualitative research work?

Hi, I am conducting an exploratory research with qualitative in-depth interview approach to understand the impact of COVID_19 in health systems response to burn care in India. Since, this is a...

19 February 2021 4,562 4 View

How to model rupture in geogrid in abaqus?

Hi researchers I wanna model tensile test on geogrid in abaqus, so I added displacement to one side of geogrid and the other side of geogrid is constrained completely, everything seems normal but...

19 February 2021 2,195 2 View

Will SARS-CoV-2 Spike be broken into S1 and S2 by denaturing conditions?

Hello, I am performing a western blot of my SARS-CoV-2 Spike-pseudotyped lentiviral particles. I denature my virus by adding concentrated virus to 2X Laemmli buffer at 1:1, then boiling for...

17 February 2021 4,844 4 View

Which CGRP I could use to treat murine cells in vitro?

Does anyone worked with CGRP on mice. I m stuck with which the product good to use. I found Sigma products are good but Sigma has a lot of CGRP products and papers didnt mention the code or cat#...

16 February 2021 8,344 2 View