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Questions related from Angana Ray
I looking for a book and corresponding book chapter that contains 1 letter RNAmods code. E.g., modification pm4,4Cm is represented as β, modification N2,N2,7-trimethylguanosine-5’-monophosphate is...
22 September 2023 1,434 0 View
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 5,969 1 View
I have a set of 2000 sequences. In that set there are two sequences >Seq1 AAAAAAAAAAAAAAAAAAAAAAA >Seq2 UUUUUUUUUUUUUUUUUUUUU When clustering with Cd-hit-est with default options, these two...
28 February 2023 793 1 View
I am doing clustering with CLANS (MPI Bioinformatics toolkit). After I launch CLANS from the command line as follows: java -Xmx4G -jar clans.jar -load xxx.clans I need to initialize and start...
09 December 2021 3,345 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 291 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 6,156 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 4,029 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 9,457 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 9,310 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 7,260 2 View
Hi I would like to get he recent amber force field (topolgy-parameter) for performing MD simulations of RNAs containing modified residues. More importantly how to simulate system containing...
29 May 2017 4,228 1 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 8,282 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 5,251 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 6,347 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 311 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 6,945 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 2,984 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 9,752 1 View
I want to do Steered Molecular Dynamics with umbrella sampling. Can anyone help me with examples or scripts ?
21 November 2013 4,427 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 4,971 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 8,336 1 View
How can we apply a constant force on a single atom for carrying out MD simulation using NAMD?
12 September 2013 4,053 6 View
The electric potential given in the output of g09 job is in atomic units, how can that be converted into SI-units
11 September 2013 6,979 0 View
While using keyword Pop=ESP in the input file for running g09, the job gets terminated showing an error message. It happens only when the molecule has potassium atom in it. The error message is...
10 September 2013 5,903 7 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 973 3 View
