Praval Pratap Singh

10 Questions 6 Answers 0 Followers

Questions related from Praval Pratap Singh

Could anyone provide CIF files of α, β, and γ-graphyne structures?

Dear ResearchGate community, If anyone within the community has access to or can provide these CIF files, your assistance would be greatly appreciated. Additionally, any relevant insights or...

02 March 2024 8,194 0 View

How to plot the phonon dispersion ?

I have done the ph.x , q2r.x , and the matdyn.x commands for a system that I am currently working on. All the three codes ran error free. Now, what is the next step to plot the phonon dispersion?...

19 May 2023 9,733 1 View

I am running protein-ligand simulation in GROMACS. My ligand_ini.pdb and ligand.gro files are not generating properly.Can someone help?

After running of python script downloaded from MacKerell lab website a file is generated: ligand_ini.pdb. After viewing it in VMD it does not look like the ligand any more.There is no error in...

03 May 2023 3,114 2 View

How do I make a bash script to execute gmx mdrun for generating checkpoint files in the interval of 1 min?

There is an error in my bash script. Here, I have taken i as the variable. And I expect to have -cpi md_0_1.part1.cpt and -cpo md_0_1.part2.cpt in the first command, gmx - cpi md_0_1.part2.cpt and...

26 April 2023 3,173 0 View

How much mpi and openmp should i give for band calculation in burai of heterostructure unit cell consist of 118 molecules ?

the workstation I'm using contains 32 core k points - 3 3 1 energy cutoff - 40 .

20 April 2023 9,385 2 View

How to solve this Ryckaert-Bellemans error?

I have a question? Command line: gmx grompp -f ions.mdp -c **solv.gro -p topol.top -o ions.tpr Ignoring obsolete mdp entry 'title' Ignoring obsolete mdp entry 'ns_type' Setting the LD random...

18 April 2023 7,986 2 View

Are there any webservers which can be used to find RNA binding site of a protein using the protein sequence?

I am working with a protein whose structure is not available in PDB, and I wanted to know if it is possible to find the protein residues which are RNA binding.

01 April 2023 8,950 5 View

How to overcome this error?

I installed autodock and now on running it on linux it gives an error on startup asking for registration and when i try to register it cannot connect to the database.

01 March 2023 7,339 1 View

I want to convert my atomtypes according to required forcefield ?

There are approx. 1,07,000 atoms in my pdb file and I am trying to replace my atom types according to the forcefield I am using. For example P --->P21 C101 ---> C11 O21 --->...

15 January 2023 9,215 2 View

How to calculate rotational diffusion in gromacs?

I just want to know if there is any gromacs command or I have to write a code

08 January 2023 8,545 1 View