Cpptraj: RMSD as a function of Residue Number?

I have the AMBER 10ns MD trajectory, I want to calculate the average RMSD over all snapshots for each residue. Would you please tell me where I can get the cpptraj script to plot RMSD vs Residue...

10 November 2016 4,533 3 View

Gnuplot: simultaneously multiply and divide $1 in gnuplot.

Hi! Can someone tell me how I can simultaneously multiply and divide $1 in gnuplot, like I have divided $1 previously using following script without rewrite data file. splot 'dssp.gnu' using...

10 November 2016 1,353 3 View

Multiply whole column with a value (Shell Programming and Scripting)?

07 August 2016 4,716 2 View

Query regarding MD Simulation of a protein with an elongated active site?

Dear all,I am interested to run MD simulation to look closer into the mode of interactions between different ligands and protein. My target protein is a homotetramer and I have selected it's chain...

06 July 2016 9,530 12 View

Troubles in understanding, amber minimization input?

Dear all, I am a beginner at amber and I have some troubles in understanding, amber minimization input file flags. I am using the following script for minimzation, Minimization Amber12 &cnrl...

31 December 2015 1,806 2 View

Any advice on the atom type error after resp charge calculation using gaussian?

I want to optimize reference ligand of my target protein (1M48) before running Molecular Dynamic Simultion. I have prepared reference ligand mol2 file through moe and then convert it into com...

11 December 2015 7,127 3 View

NAMD tuitorial for Membrane Bound Protein Complex Structure.

03 April 2015 6,859 2 View

Is the aminoacid sequence of PDE-1 type 5 venom of Bothrops atrox available?

I am unable to find amino acids sequence of PDE-1 type 5 venom of bothrops atrox in any sequence database. I am interested to target this protein for computational studies. Kindly guide me, if...

31 December 2014 2,003 3 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

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

How to repeat an operation on an atom selection for multiple times in PyMol?

Hi, I am trying to construct a multi-layer fibril structure from a single layer in PyMol by translating the layer along the fibril axis. For now, I am able to use the Translate command in PyMol...

02 March 2021 4,569 4 View