How can I convert an enzyme pdb file into a topology file for GROMACS use?

More Manoj Kumar Mahapatra's questions See All

Why the ligand structure changes during molecular dynamics simulation?

I did MD simulation for 10 ns. the ligand was inside the simulation box upto 10ns. only in the 3rd ns the structure was ok. in all other time one of its double bond was missing. many times the OH...

11 December 2015 3,695 7 View

How can i extract the ligand-receptor docked file and save it in pdb in GLIDE (shcrodinger) docking?

I want to take the pdb file of ligand-receptor complex for MD simulation in GROMACS.

07 August 2015 8,619 0 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

For an in-vitro drug release study, what molecular weight cut-off (MWCO) dialysis bag is required for a 117 kDa protein?

kindly reply me. Thanking you in advance.

05 August 2024 7,727 4 View

Inquiry on Maximum Nucleic Acid Volume for 2.5 mL Liposome Solution?

I am currently working on a project involving liposomes and need to determine the maximum volume of siRNA that can be added to a 2.5 mL liposome solution with a total lipid concentration of 10...

30 July 2024 6,420 1 View

CAD File of human's & rat's respiratory airways ?

Dear all, I am working on particle deposition in human's & rat's respiratory airways using CFD and I am looking for the 3D CAD file for my simulations (STEP or IGES format). If somone has such...

29 July 2024 1,092 2 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

Could someone please provide a list of journals that accept the application of methodologies in nature-based solutions?

I am looking for journals that admit the publication of results from applying the IUCN Standard for designing and monitoring Nature-based solutions. Many thanks for considering my request.

23 July 2024 6,444 2 View

MDCI module in Orca software?

Dear Researchers, My question is associated with the "MDCI" method in Orca. Please let me clarify my question using a simple example: Suppose we are going to perform CBS extrapolation using "!...

21 July 2024 1,632 0 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

Ranylson Marcello Leal Savedra

Dear Manoj,

use the tool pdb2gmx (GROMACS). I have attached a website to illustrate how to use this tool.

http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/lysozyme/01_pdb2gmx.html

Meenu Sharma

its a wonderful turorial. thanks.

but prodrg server is not working now a days. is there any other option to convert ligand coordinates from pdb to gro format.