Vikas Kumar

7 Questions 12 Answers 0 Followers

Questions related from Vikas Kumar

How to generate topology for Graphene molecule from .gro file using GROMACS program?

Greetings, everybody. I have generated a graphene sheet using the VMD program and saved the resulting file in the .gro format. Now I would like to use the GROMACS program to model the interaction...

18 December 2023 8,134 1 View

What would be the optimal way to convert a 2D .sdf chemical library into .pdbqt for AutoDock Vina docking?

I am attempting to convert several .sdf ligands (2D) into .pdbqt files using the Open Babel program for molecular docking. I have followed the steps below: Add Hydrogens Generate 3D...

05 October 2023 1,525 3 View

Is there any online webserver which can be utilized for blind docking for ssDNA-ligand docking?

Hello everyone I want to know is there any online webserver which can be utilized for blind docking for ssDNA-ligand docking?. I have tried few protein-protein or protein-DNA compatible webservers...

08 November 2021 1,012 5 View

Fatal error: Syntax error - File LIG.itp, line 7 Last line read: '[ atomtypes ] ' Invalid order for directive atomtypes ?

Hello everyone, I am trying to simulate the protein-ligand complex with Zn ion but during solvation i am getting the following error: Fatal error: Syntax error - File LIG.itp, line 7 Last line...

16 April 2021 4,720 1 View

Fatal error: Atom OXT in residue PRO 372 was not found in rtp entry PRO with 14 atoms while sorting atoms ?

Hello everyone i am trying to generate topology file of Protein DNA complex but my protein structure have some problem in PRO 372 residues someone please suggest the solution for this I will be...

22 June 2020 1,741 1 View

While performing energy minimization step in GROMACS I am getteing following error. Can anyone help with this minimization problem?

gmx mdrun -v -deffnm em Back Off! I just backed up em.log to ./em.log. Running on 1 node with total 8 cores, 16 logical cores Hardware detected: CPU info: Vendor: GenuineIntel Brand:...

12 March 2020 3,128 1 View

In silico AMDET properties how P-glycoprotein substrate and Inhibitors can affect the drug distribution.

I need your opinion on ADMET properties. If one drug is a substrate of P-glycoprotein and also an inhibitor of P-glycoprotein1/2. Then what are the consequences of this behavior. Is this mix...

01 January 1970 6,429 2 View