Hi, I am Gourav, a PhD student from IIT Kharagpur, India. In this channel, I will upload tutorials on different computational chemistry tools including AMBER, gaussian, and pymol. Alongside the tutorials, I will also discuss various topics on Biochemistry.
@@mdwithgourav9263 Did it the way you suggested. Then I cleaned and symmetrized the compound in gaussview and saved it in mol format for energy minimization in Gabedit which worked too. But when I try to open the energy minimized file(mol) in gaussview it says 'Failure reading molecules from MDL file'
Thank you sir very much for your insightful videos. Can you please guide on the issue: Methane forms a T shaped complex with benzene (with its pi electron cloud), then how can i scan the distance of methane from the center of ring (benzene) to construct a potential energy curve? It will be great help.
My submit button can’t be tap because i can’t install gaussview, Said that this app can’t run on ur pc, check the software publisher. How to fix it sir?
Hi, i have a doubt regarding the charge of the molecule. my ligand have charge so i need to add ions to it . can you please tell me how to add ions like chlorine and sodium
Hii! I am facing a totally different problem, not related to this tutorial. So I have a docked complex, and after solvating when I am visualizing it in pymol or chimera or vmd, the unit cell boundaries are totally out of my solvated strucutre. Can you please help? Thank you :)
Hey! How to strip water from my prmtop and mdcrd file? I ran an MD simulation using Amber 20 and I just want to look at my peptide and therefore need to strip water. I tried using parmed but I get an error saying that the parmed command does not exsist. Can you help? Thank you!
To strip water from prmtop and mdcrd files, you have to use parmed and cpptraj respectively. If parmed is not opening then kindly check whether Amber20 is properly installed or not. Also, you can try to source the amber.sh file.
Yes, you can create the prmtop and rst7 files of the complexes. But first you have to generate the modified forcefield parameters of the ligand/small molecule using Antechamber.
Hi Mr. Gourav! Can you share how you got access to Gaussian View? I wanted to perform theoretical calculations and Gaussian View is such a good aid to set up the files and visualize everything. Thank you!!
Hi Gourav, Its nice to see your videos on AMBER. Can you please make a playlist of your AMBER videos in step by step order of protein simulation and Protein ligand simulation?
@@chaymaesa4638 It depends on the number of atoms in the system. For larger systems (molecules with around 100 atoms), you have to increase both the processors (try with atleast 16) and memory (may be 5 GB). So, it would be better to use supercomputer server.
Nice explanation, please make video on how we can find the Gibbs free energy , Enthalpy, Zero point energy and deformation energy using gausison package.
Thank for your tutorial! sir i have a DNA + protein duplex in this case what I do using force field? source leaprc ff19SB (protein) source leaprc water.opc or source leaprc ff19SB source leaprc.DNA.OL15 source leaprc water.opc
@@mdwithgourav9263 Thank you sir ! I have one more question. In my case DNA + protein pdb Does the protein force field affect dna in Amber? The opposite is the case (whether the dna force field affects the protein?) I want to know if the force field applies individually.
