How can I get topology file for my ligand molecule?

More Amali Guruge's questions See All

How do we do micelle clustering and how do we make index file for molecules in micelles?

My system contains three micelles. I want to calculate radius of gyration for each micelle in the system. I did the micelle clustering, but I am struggling with the step 3 in...

07 August 2018 2,635 1 View

How can I model a hexagonal phase using Packmol?

Dear All, I want to arrange my surfactant molecules in a hexagonal arrangement for my MD simulation. Appreciate, if anyone can guide me to do that. Thank you.

06 July 2018 8,423 2 View

How to solve the Gaussian error; Water molecule starting at atom 93528 can not be settled?

Dear All, My system contains water molecules and polyethylene glycol molecules. I generated the box (15.2*15.2*15.2 nm*3) using genbox command. Thereafter, PEG molecules were added using gmx...

09 October 2017 7,074 0 View

What should I assign to pcon and ncon in polar.mdp in g_mmpbsa?

Dear All, In my MD simulation I only added counter ions (20 Na+ ions) to neutralize the system. Now I want to do MM_PBSA calculations for my MD runs using g_mmpbsa. In order to do perform polar...

06 July 2016 7,537 1 View

Can we do molecular docking in the presence of crystallized water molecules using DOCK6?

Dear All, I want to do molecular docking processes for an enzyme and ligands in the presence of co-crystallized water molecules (of the enzyme) using DOCK6. Can anyone help me? Appreciate if...

05 June 2016 2,615 0 View

How to get publication quality images in PoseView?

Dear All, I want to get high quality images of 2D pictures generated by PoseView software. Can anyone help me? Thank you.

05 June 2016 6,125 1 View

How rmsf of linker doamin in human topoisomerase I change with the binding ligand?

Dear All, I completed molecular dynamics for three ligands, T1L25, T2L25 and T3L25 using GROMACS software with CHARMM27 force field. How can I explain the rmsf behavior of linker domain (linker...

03 April 2016 5,113 5 View

Ligand interactions with DNA

Dear All, I have two receptor-ligand complexes. In one system, the ligand intercalates in DNA and from two hydrogen bonds (one with the enzyme and one with DNA duplex). In other system, the ligand...

02 March 2016 329 4 View

How can I use the itp file generated from SwissParm for MD simulation using GROMACS?

Dear All, I used SwissParm to generate CHARMM itp files for my ligand molecules. I used GROMACS for molecular dynamics simulations. After getting the itp file for the ligand, I used that file...

11 December 2015 3,606 0 View

How can we convert pdb structure to Gromacs when it contains DNA?

I want to convert the pdb format of topoisomerase I into Gromacs.The pdb id for the structure is 1K4T. I removed ligands, water and Hg ion from 1K4T. But DNA is required for the MD simulation. I...

08 September 2015 5,092 1 View

MD MOE RMSD

How to calculate the RMSD values for a MD simulation using MOE?

07 August 2021 0 0 View

MD MOE RMSD

How to calculate the RMSD values for a MD simulation using MOE?

07 August 2021 0 0 View

fatal error

When I tried to energy minimization my system, I got fatal error as below. Fatal error: Atomtype opls_116 not found Although I've already added this line: ; include water #include "oplsaa.ff/spc.itp" to [molecultype] directive in my topology.

16 June 2021 0 0 View

fatal error

16 June 2021 0 0 View

fatal error

16 June 2021 0 0 View

fatal error

16 June 2021 0 0 View

How to analyze a particular region of my simulation box in GROMACS?

Hi, I am using GROMACS 5.1.4 to simulate water in contact with a surface. I am only interested to calculate some properties of water near the surface. Let's say at a distance of x nm from the...

03 March 2021 9,989 2 View

What kind of fluid could I use for a pitfall trap that also does not invalidate molecular testing?

Hi, I want to start testing pitfall trap to obtain ants samples, but I need to conduct molecular analysis on those insects. So, what kind of fluid can I use? Ethanol expires too early and I need...

03 March 2021 5,978 5 View

Arena simulation - how do i model the following model in ARENA (see description) (new to ARENA)?

Hello, I'm fairly new to ARENA and I have the following problem: I have two queues in which, in each queue, a different order type arrives (both having an arrival rate of exponential 10). Order...

02 March 2021 2,431 3 View

Why are the velocities so high in my Boussinesq approximation Fluent simulation?

Hello, I have a mechanism where air rises due to convective flows. In this simulation, nothing is driving the air except this. I understand that the Boussinesq approximation only works for small...

02 March 2021 4,910 3 View