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

More Shreyasi Asthana's questions See All

Has anybody tried infecting a virus compatible cell line with serum derived virus?

I am trying to infecting huh 7 cell with plasma derived HCV but the infection cannot be established. Has anybody tried infecting any cell line with virus derived from plasma/serum?

03 April 2024 4,685 0 View

Zebrafish Heart histology, tissue prep going wrong. Where from I can get technical advice?

Zebrafish heart is very small, Like a pinhead. We are trying to make histology of zebrafish hearts but facing problems. organ fixation is going well but after block prep tissue is becoming...

27 June 2023 9,535 3 View

Can anyone help me in identifying the fungal spore with hyphae?

Fossil leaf-borne fungus recovered from Neogene sediments. Hyphae septate, spores in clusters, with multiple folds.

07 June 2022 9,662 0 View

How to import SEM images into GDSII editor in Raith Pioneer software?

I have been trying to connect 2D materials with pre-patterned bigger Au pads on SiO2/Si substrate using the Raith Pioneer electron beam lithography system. I am facing difficulties in importing...

13 December 2021 9,634 1 View

How to add switch on feed strip of a microstrip patch antenna using HFSS software?

I am working on a 2x2 microstrip patch antenna design using HFSS software. I have completed the design of the antenna. I want to somehow add switches to the feed strip of each of the 4 individual...

23 November 2021 6,440 4 View

I need a proper step by step tutorial for proper forest plot formation in metaanalysis of biological data. Can anyone help me?

In metaanalysis or systematic review, forest plots are made to compare different data set as random trial. I need to learn that .help needed.

03 July 2020 9,735 4 View

Is modulation index of 0.99 justifiable (SPWM) for three phase grid tied inverter If Operating frequency is 50KHz and SiC mosfets are used?

Specifications: Grid Voltage 415 V(L-L) Operating Frequency- 50 KHz DC Bus- 600V to 1000V pf=1 For Three phase grid connected inverter, and minimum DC bus voltage of 600V (from PV panel),...

05 May 2020 6,651 0 View

How to deal with missing data in a meta analysis ?

Sometimes details on outcome variable is not provided how to deal with such data.

15 May 2018 2,546 3 View

I tried to isolate full immature gonad from 20-30day fish but failed . plz anyone help me or guide me how to dissect out it .

fish gonad become mature andobservable after sexual maturation but . there are many papers in juveniles ..I want to know how they dessect it out properly .any suggestion or link would be...

30 July 2017 8,903 3 View

Does Propidium Iodide specifically bind to dead cells?

Hi everyone I am trying to perform live dead assay in a mammalian cell line. I am using DAPi and PI, i.e. ideally DAPI staind nuclear material in all cells and PI must stain nuclear material of...

23 March 2017 556 6 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

Justin Lemkul Popular answer

http://rashmikumari.github.io/g_mmpbsa/

Justin Lemkul

Sidra Rafi

http://www.sciencedirect.com/science/article/pii/S0010465514003154

Mayur Mukhi

Justin Lemkul How do I know how much of the trajectory or how many frames I should use for the MM-PBSA analysis?

Fatemeh Haghighi

Check the RMSD

Fatemeh Haghighi How do I tell from the RMSD? Could you please elaborate. Thanks in advance!

You should take the period where RMSD of the protein is stable.

Fatemeh Haghighi Got it. Thank you very much!

You're welcome