How to perform molecular dynamics simulation of Protein-RNA complex at different pH condition??

04 May 2017 8,319 4 View

How do I perform protein-ligand simulation in gromacs with gold atoms?

I want to run protein-Ligand simulation where gold atoms are ligand. Gromacs is showing error for that. I tried to use Prodrug server also, but it is not generating coordinates for gold...

10 November 2015 4,290 7 View

How can I build the virion capsid from single coat protein?

I am having the full-length homotrimer coat protein's predicted model. I want to rebuild virion capsid (Icosahedral virion) by using this homotrimer. Capsid structure of this virion is available...

10 November 2015 9,219 3 View

Can anyone tell me protein's name whose three dimensional structure contains Gold atoms?

10 November 2015 7,672 1 View

Is there any kind of change in pH of cell while it is dying due to viral infection?

31 December 2014 4,222 11 View

What is the relation between stability of protein and Gibbs free energy?

If conformational changes are occurring in protein structure then how will it effect Gibbs free energy of that particular protein?

10 November 2013 8,543 14 View

How to predict protein structure along with dsRNA?

I want to model one protein structure along with Double strand RNA molecule. I tried to dock this RNA in protein with the help of HADDOCK server but it is not giving the exact pose which I needed...

07 August 2013 1,636 4 View

How do I infer energy landscape in Dihedral Principle Component analysis in Gromacs?

I am performing MDS to find out conformational changes in protein structure. To verify that result, I have done Dihedral Principle Component analysis (DPCA). I got the result up to energy...

06 July 2013 4,457 0 View

How to do multi-chain and multi-template modeling at same time in modeller?

I want to do multi-chain modeling by using more than one template at one time. How should I do this? Do I need to change model_multiple python script or to change model_multichain script?

05 June 2013 8,949 2 View

I am facing some problems while running a pH dependent simulation of homotrimer. Can anyone help me to solve the given error below?

Fatal error: There is a dangling bond at at least one of the terminal ends. Select a proper terminal entry.

05 June 2013 2,554 4 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

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