19 Questions 27 Answers 0 Followers
Questions related from Angana Ray
I want to simulate RNA molecules containing modifications such as PSU with amber ff and GROMACS software. I have the gromacs compatible amber14sb_OL21.ff from https://fch.upol.cz/ff_ol/gmxOL21.php...
16 March 2023 5,894 1 View
I have two PDBs: PDB ID 4TS0 and PDB ID 3SUY. Both these are RNAs, and both contain the residue CCC. However, when I open the PDB file, I see the line "MODRES 3SUY CCC X 101 C" in case of 3SUY...
01 March 2021 223 1 View
I am planning to do MD simulation of IDPs using charmm36m force field. The software I am planning to use is GROMACS 2019. Hence, my question is how do I get the charmm36m force field in GROMACS...
26 February 2020 6,063 4 View
I am trying to do PCA from the MD trajectory of a multi-domain protein using GROMACS tools. I am using gmx covar and gmx anaeig for PCA. My protein has many domains, but I would like to focus on...
25 December 2019 3,928 4 View
After about 600ns of my MD run, I notice that my molecule has started interacting with the image. I understand that I should use a larger box length but is it possible for me to continue the MD...
25 March 2019 9,382 2 View
I am using GROMACS2018 with amber14sc_parmbsc1 force field for simulations. I have DNA,RNA,protein,NA,MG and water in my system. I want to analyze my trajectory. the way I have written my...
30 January 2019 9,244 3 View
My systems contains proteins + Nucleic Acids + Mg2+ ions. First I solvate this using gmx solvate and then I try to neutralize the system using gmx genion with the option "-neutral". However, I see...
10 April 2018 7,205 2 View
I have performed MD simulation with RNA (3 strand helix) using GROMACS. During MD-run the strands are separated due to PBC and also broken during PBC. How to "unwrap" or make the molecule...
26 May 2017 8,209 3 View
I did simulation using NAMD and wrapall = on option. While saving the coordinates in pdb format from the trajectory format, I want to unwrap the molecule.
08 August 2014 5,171 5 View
I have simulated a protein molecule. I need to calculate the side chain torsion angles along with main chain torsion angles for all/or any particular residue(s). I am trying to use a tcl script.
11 April 2014 6,285 3 View
I have done SMD of telomeric quadruplex DNA using NAMD software, GBIS implicit solvent model and CHARMM-27 ff. I have pulled the center of mass of the 1st base keeping center of mass of the last...
14 February 2014 252 1 View
I have already started quantum studies on graphene sheets. I have optimized graphene and GO sheets using DFT and b3lyp,wb97xd basis sets. Apart from optimization I am a little confused as which...
05 December 2013 6,874 2 View
I am doing SMD of protein using NAMD and CHARMM ff. I have an output file which gives the 3 components of force applied and coordinates of the atom on which force is applied for various snapshots....
29 November 2013 2,925 4 View
I am doing SMD of protein using NAMD with constant velocity pulling. In order to do the simulation, we have to specify the smd-atom (the atom to which the dummy atom is attached and then pulled)....
22 November 2013 9,693 1 View
I want to do Steered Molecular Dynamics with umbrella sampling. Can anyone help me with examples or scripts ?
21 November 2013 4,340 1 View
I have done SMD of protein at applying constant velocity using NAMD software and CHARMM ff. Since, this is my first time in performing Steered MD, I am not sure as to should I do umbrella sampling...
20 November 2013 4,914 3 View
I am trying to strudy force induced unfolding of protein by constant force SMD Simulation using NAMD. I have used GBIS, because the water model is not possible. I see that my protein completely...
30 September 2013 8,261 1 View
How can we apply a constant force on a single atom for carrying out MD simulation using NAMD?
12 September 2013 3,984 6 View
Molecular Dynamics Simulation is done by CHARMM and Constant Force is applied on one atom each of the two terminal bases.
02 September 2013 903 3 View
