How would I do MM-PBSA analysis after MD simulations in GROMACS?

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How to culture MIN6 cells?

Hello everyone!! I am trying to grow MIN6 cells, but I am unable to. The growth rate is too slow. I can hardly see 5-6 cells in the plate. Also the morphology of the cells is highly irregular. I...

07 August 2018 7,422 3 View

How to write a thesis title?

Can a thesis title be a question?

08 September 2017 7,161 2 View

Do Min6 cell lines adhere to glass slides?

I wish to grow Min6 cell lines on glass slides for imaging experiments. Are these cells adherent or do I need to coat the slides before seeding cells on to them?please advise

01 February 2017 5,833 3 View

Can anyone suggest me a protocol for analysis of ROS in aqeous solutions?

Hi I want to measure ROS in a aqueous solution containing a protein and ROS generating agents in buffered solutions. Is there a protocol for the same/ and is it ok to use DCFH-DA for this? Please...

31 December 2016 1,528 0 View

What are the criteria while using a protease inhibitor?

How should I choose an effective protease inhibitor which can can be used for the purification of a range of proteins to be purified by Q-sepharose or Ni-NTA or SP-sepharose?

06 July 2016 5,200 5 View

What is the optimal staining procedure for SDS-PAGE?

I have a protein to be expressed with an apparent MW of 18.4 Kda.For that I used 13% resolving gel.I use an unstained protein ladder.After the run was over, I stained the gel with commasie.The...

06 July 2016 8,133 5 View

How long a stock solution of amyloid proteins is stable in DMSO?

I have stored a stock solution of an amyloid protein in DMSO for a long time. How long it will be stable without aggregating or forming amyloids, so that I can use it for further studies/experiments.

05 June 2016 7,601 5 View

What should be the optimum protein load (volume and concentration) when purifying a protein by sephadex G 100 , Column chromatography?

What should be the optimum protein load (volume and concentration) when purifying a protein by sephadex G 100 , Column chromatography Any suggestions would be highly appreciated :)

31 December 2015 7,451 3 View

What is microfluidic protein sizing?

Can anyone explain me what is the meaning and principle of microfluidic protein sizing

11 December 2015 4,706 4 View

How might I calculate Guanidinium concentration in molecular dynamics simulation of proteins?

Hi everyone!! While performing the MD simulations on proteins and studying their unfolding by Guanidium, How should one determine the guanidium concentration with regard to the number of molecules...

06 July 2015 4,535 3 View

Gromacs first step of minimization ?

I have face this problem anyone help me how to solve this issue ?which is below Fatal error: There are inconsistent shifts over periodic boundaries in a molecule type consisting of 78 atoms. The...

07 August 2024 2,598 1 View

How to restart MD without using checkpint file in GROMACS?

Dear All Gromacs User I would like to restart MD without using checkpint .cpt files? I heard there is a way for acheiveing this. Any input and sugegstions are most welcome. Thanking You Budheswar

29 July 2024 3,084 8 View

How to prepare a molecule for molecular dynamics calculations?

If I want to calculate molecular dynamics (Gromacs), do I first need to optimize the geometry of the molecule? For example, I first draw the molecule in Avogadro, and then what? I guess I can't...

28 July 2024 673 3 View

Wrong out put for gmx x2top?

Dear users, I would like to simulate a zeolite structure in gromacs. I got the .cif file from IZA expanded in one direction in Materials Studio and exported a .pdb file. However, when I want to...

24 July 2024 367 4 View

Why binding energy is in positive number after performing mmpbsa?

I performed mmpbsa of protein-protein complex simulation on gromacs. My binding free energy is +166781. This complex is stable when experimentally produced in wet lab. In index.ndx I grouped...

19 July 2024 4,120 5 View

How to resolve ‘[ atomtypes ] Invalid order for directive atomtypes’ error in Gromacs?

I have been using Gromacs 2021.7. I wanted to simulate two small molecules in water. But, while generating the ions.tpr, I am getting the following error. The topol.top and .itp files for each...

17 July 2024 9,897 4 View

Getting this error : gmx_mpi': corrupted size vs. prev_size: 0x0000000001d1b320 ***?

i am using the trjconv command in gromacs gmx_mpi -debug trjconv -s md.gro -f md.xtc -o utr.xtc -fit rot+trans and after few steps i got the error gmx_mpi': corrupted size vs. prev_size:...

17 July 2024 6,216 1 View

Can we find the Gromacs version from XTC file or TRR?

Hello everyone, This soudns like a strange question, but I created five XTC files using five different versions of GROMACS some years ago. All other files are missing, and I want to repeat the...

16 July 2024 7,205 2 View

How to define a zeolite structure with rigid framwork?

Dear Gromacs users, I would like to simulate a zeolite-water system. In different literature, it is suggested to consider a rigid framework of zeolite to decrease the computational cost. I would...

15 July 2024 4,590 1 View

In silico techniques for identification of inhibitor/activator/substrate activity?

Hello dear researchers, I would like to know about available in silico tests that could predict the activity of ligands (small molecules) against the target protein. I have performed docking...

08 July 2024 4,724 4 View