Could anyone suggest suitable tools to plot protein contact maps?

My protein is 476 residues. I would like to plot the map only for specific regions and mention it in the input thus choosing the residues i wish to calculate the contacts for. Does anyone know of...

10 November 2014 6,355 9 View

Radius of gyration as a measure of protein compactness - does it apply to only globular proteins?

09 October 2014 6,980 6 View

Can anyone assist me with adding probability of state on the projection of eigen vector PC1 vs PC2 plot in gromacs?

I have performed the principal component analysis in gromacs and I have obtained the projection of eigen vectors PC1 vs PC2 plot as in figure 4BI would like to add information about the...

08 September 2014 4,787 5 View

Is it possible to find out the occupancy of water within a protein using gromacs?

I would like to plot no. of water molecules within a cut-off distance as a function of time. Any gromacs utility that will help me? Thanks in adv

08 September 2014 5,231 5 View

Do all proteins with a beta- barrel (Fec A transporter) or half beta barrel (cystatin) necessarily twist?

08 September 2014 5,788 2 View

Is anyone aware of names of proteins that show large bending movements that are functionally relevant?

I would like to get the names of a few proteins that show bending dynamics in solution. Are there any transport proteins that shown similar movements? Kindly post them here. Thanks in advance.

05 June 2014 6,702 8 View

How can I deal with the substrate moving out of the box during MD simulation?

I have simulated an elongated protein in a cubic box (reason being the long edges of the protein tilt during simulation and interact with its periodic image thus resulting in bad energy values...

05 June 2014 7,835 5 View

What is the energy barrier from hinge movements (like bending and twisting) in proteins?

In two domain proteins there are movements possible along the hinge. Is anyone aware of the energy involved in this hinge movement?

05 June 2014 9,906 9 View

Is anyone familiar with the methodology/tool to calculate twisting in proteins?

I wish to calculate the extent of twisting that my protein undergoes. Is there a tool/script/software that will enable this calculation? It is a beta barrel domain of the protein that is...

03 April 2014 8,700 3 View

How do you compute rmsd using ptraj in Amber software?

How do I specify this in the mask for AMBER ptraj? Protein residues are from 1-400. But I want to leave out two loop regions,100-105 and 250-255. The RMSD plot fluctuates and I presume leaving out...

03 April 2014 618 28 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

Enhanced Yellow Fluorescent Protein (Aequorea victoria) DNA sequence?

I am on the lookout for the Enhanced Yellow Fluorescent Protein (Aequorea victoria) DNA sequence. Does anyone know where I can find it? Thank you in advance

03 March 2021 3,568 1 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