Problem with H-bond analysis in GROMACS ?

I have simulated a protein-protein complex in GROMACS. During Hydrogen bond analysis for individual residues using gmx hbond, I am getting results as H-bond average 1.012 for 2134 frames. What to...

11 December 2016 6,634 5 View

How to model a nanoparticle computationally ?

I want to study interaction studies of nanoparticle with my protein of interest. can anyone suggest me how to model a perfect nanoparticle for computational studies? what shall be the parameters...

06 July 2015 6,432 2 View

How can I dock multiple ligands to each pocket of each monomer of a homotetrameric protein?

I am trying to dock ligand to a homotetrameric protein which is functional only in its tetrameric form. My problem is I have to dock four ligands in the four catalytic pockets of each monomer....

01 February 2015 2,654 5 View

Protocol for inner and outer membrane isolation from Bacillus subtilis

06 July 2014 6,936 1 View

What are the best methods for removing contaminating gDNA from my RNA preparations which I will be using for RT-PCR?

See above.

05 June 2014 4,118 20 View

I am unable to see any band for my PCR?

The annealing temperature of the primer is very low (35 degrees centigrade). What should be the measures? Should I redesign my primers?

11 December 2013 4,207 11 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

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

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

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

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

What techniques can I use to determine the miscibility of polymer blends?

The term miscibility refers to the single-phase state in thermodynamics. I do not mean the compatibility of different components. To determine the miscibility I know several techniques such as...

03 March 2021 4,107 4 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