Jan 25, 2023
Protocol 2: MD simulation with Gromacs
- Phaniendra Alugoju1,2,
- Vishwambhar Vishnu Bhandare3,
- Vishal S Patil4,5,
- Krishna Swamy V K D6,
- Prem Kumar Borugadda7,
- Tewin Tencomnao1,2
- 1Department of Clinical Chemistry, Faculty of Allied Health Sciences, Chulalongkorn University, Bangkok, 10330, Thailand;
- 2Natural Products for Neuroprotection and Anti-Ageing Research Unit, Chulalongkorn University, Bangkok, 10330, Thailand;
- 3Department of Microbiology, Shivaji University, Kolhapur, Maharashtra, 416004, India;
- 4Department of Pharmacology and Toxicology, KLE College of Pharmacy Belagavi, KLE Academy of Higher Education and Research (KAHER), Belagavi, Karnataka, 590010, India;
- 5ICMR-National Institute of Traditional Medicine, Belagavi, Karnataka, 590010, India;
- 6Phytomedicine and Ageing laboratory, Department of Biochemistry and Molecular Biology, Pondicherry University (A Central University), Puducherry, 605 014, India;
- 7Department of Computer Science, School of Engineering and Technology, Pondicherry University (A Central University), Karaikal Campus, Karaikal 609605, India.
Document Citation: Phaniendra Alugoju, Vishwambhar Vishnu Bhandare, Vishal S Patil, Krishna Swamy V K D, Prem Kumar Borugadda, Tewin Tencomnao 2023. Protocol 2: MD simulation with Gromacs . protocols.io https://dx.doi.org/10.17504/protocols.io.36wgqjmp5vk5/v1
License: This is an open access document distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited
Created: January 25, 2023
Last Modified: January 25, 2023
Document Integer ID: 75842
Abstract
Structural stability of the docked complexes was monitored using MD simulation with Gromacs 2020.5 (RRID:SCR_014565). The protein topology was created using Gromos96 force field and the PRODRG server was utilized to create the topology of the ligand. The docked complexes were solvated using ‘Simple Point Charge’ (SPC) water model in a cuboidal box with adequate size to accommodate the complete complex at the center.The modeled systems were neutralized using required number of counter ions (Na+ / Cl-). The undesirable contacts and steric conflicts were then removed from the neutralized systems using steepest descent followed by conjugate gradient methods for 50,000 steps each. The NVT ensemble used to maintain constant number of atoms, volume, and temperature, further NPT ensemble was used to maintain constant pressure. NVT and NPTensembles were used to maintain temperature. The temperature and pressure were set constant at 300K and 1 bar respectively, during the equilibration of 1ns. Further, followed by 1ns of equilibration, unrestrained MD simulation was performed for a period of 100ns in solvent. The Particle Mesh Ewald (PME) method was used to handle coulomb electrostatic interactions, while the LINear Constraint Solver (LINCS)s algorithmwas used to limit H-bonds. Using a cut-off value of 14 Å, the non-bonded contacts were trimmed. The trajectories generated were analyzed using some of the inbuild gromacs tools like ‘gmx rms,’ ‘gmx rmsf,’ ‘gmx hbond,’ ‘gmx gyrate,’ ‘gmx sasa,’ etc. and other additional packages for specific analysis wherever required. Conformational changes at the secondary structural level were monitored by using Dictionary of Protein Secondary Structure (DSSP) software (RRID:SCR_002725).
Protocol 2 MD simulation with Gromacs .docx