How can I calculate center of mass for a protein?

Hello every body I want to calculate the center of mas for a protein. I want to know which amino acid the center of mass hold on. pleas give me a full help. thanks

31 December 2017 328 8 View

How can you calculate salt bridges and hydrogen bonds for a specific part of the structure in throughout a trajectory?

Hello every body I want to calculate the pattern of salt bridges and hydrogen bonds between two specific part of the protein througut the for the 10 last ns of a gromacs simulation trajectory....

31 December 2017 217 3 View

Could i treat different stages of cancer cell line with the same drug?

Hi every body I work on Wnt/beta catenin signaling pathway. I have a drug which is effective on non metastatic SW480 cell line. I want to test it on metastatic cell line SW620. the pathway is...

11 December 2017 1,635 4 View

How can I calculate antrophy using gromacs?

Hello every body I want to calculate the antrophy amount of a protein-protein complex using gmmpbsa module of gromacs. I can calculate binding energy but not antrophy. If you have any...

11 December 2017 8,649 1 View

How should i define a calcium in pdb file?

hello I have a protein with a calcium ion. I edited the PDB file, renaming the calcium to CA, as atom name and atom type and pdb2gmx, runs successfully. but know I worry becuse some viewers...

01 February 2017 6,703 0 View

Could any one help me in peptide expression?

I want to express a 37 a.a, 43 a.a and 55 a.a peptides using pET His6 Sumo TEV expression vector with BioBrick polypromoter restriction sites (14-S). the vector host is XL1 blue and the company...

08 September 2016 5,212 3 View

How can I calculate the dihedral angle change of two helices using amber scripts?

I need to know the position of two helices in a structure in comparison to each other. so I should to calculate the variation of their dihedral angles versus time. there is an article in the...

05 June 2016 9,713 2 View

How could i get a free clash avarage structure from gromacs trajectory?

hello I have 200 ns simulation of a peptide and i want to calculate average structure of the simulation. I used this command: g_rmsf -f md.xtc -o rmsf.xvg -s md.tpr -ox av.pdb The resulting pdb...

05 June 2016 323 4 View

How could I refold Denileukin diftitox(ontak) after extraction?

Hi is there any instruction to refold Denileukin diftitox(ontak)? it is really vital for my project. every help is appreciate.

09 October 2015 4,923 0 View

How can I set the pressure in NPT phase of molecular dynamic simulation?

We could set temperature with kinetic energy in MD. How about pressure in NPT phase?

31 December 2014 8,167 8 View

How to analyze a particular region of my simulation box in GROMACS?

Hi, I am using GROMACS 5.1.4 to simulate water in contact with a surface. I am only interested to calculate some properties of water near the surface. Let's say at a distance of x nm from the...

03 March 2021 9,989 2 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

Why almost every element would be metallized in sufficiently high pressure and low temperature?

(This statement is from wikipedia, BTW). What is so special about metallic bond that is limiting high-P low-T state of a matter (as long as individual atoms exist, not white dwarf of neutron star...

02 March 2021 3,309 2 View

Why Austenite grains in steel show much more twinning than ferrite grains?

It is oftentimes said to be a distinctive metallographic trait that differentiates a fully austenitic and a fully felly ferritic steel without etching that might distinguish between two. Why...

02 March 2021 728 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

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

How to replicate the well conditions of a crystal hit with 20%(w/v) isopropanol?

I had a crystal hit in a well with 0.1M HEPEs pH 7.5, 10%(w/v) PEG 4000, and 20%(w/v) isopropanol. Why is isopropanol in w/v here if it's just solvent? How do I recreate this well condition?

25 February 2021 9,761 1 View