How can i generate a pdb for A polyarginine peptides R8 for molecular dynamic simulation ?

More Hamid Shafiee's questions See All

How can we add peptide to charmm gui membrane system?

I made a membrane in charmm gui...I didnt pay attention to water box...I did the md run in gromacs .now I want to load poly arginine peptide above the membrane by VMD but i understood that by...

31 December 2017 2,842 3 View

How can we transfer all atom to coarse grained?

except vmd software, what are other ways to transfer all atom to coarse grained via martini tools?

10 November 2017 8,792 0 View

Modeling of thermoacoustic phenomenon in rijke tube with ansys fluent?

31 December 2015 408 2 View

Is anybody familiar with renewable energy for structures in the deep sea?

31 December 2014 6,922 4 View

About renewable energy?

I want to offer a mechanism for renewable energy production of Structures in sea with maximum 50m depth.that The structure is self-sufficient in energy supply.What strategy do you recommend to...

31 December 2014 3,934 6 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

Why does blocking with my immunogenic peptide cause nuclear fluorescence in ICC?

Hi all, I am validating a polyclonal antibody raised against human ANT4, through WB and ICC. In most of my controls, the antibody shows very little off-target binding, but when I pre-incubate the...

03 March 2021 5,999 3 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

Jamoliddin Razzokov

If you know the sequence of your peptide you can create it using Avogadro software. Just install it and after opening go to Build/insert/peptide. Then you can save the created structure in any format (e,g PDB).

Krishnendu Bera

You can do Homology Modeling or multi template modeling of your protein based on your PDB-BLAST result using Modellor software. If you are not finding satisfying similar template for your protein of interest then you can do modeling using I-TASSER like server. You can get your protein structure.

Hamid Shafiee

thanks all

Hi Mr Razzokov

I made a pbd file with avogadro software.now for making coarse-graine model in vmd i need psf file, how can i get topology file to make a psf file?

Thanks

I have never tried to do it but following this link hope you will prepare your psf file: https://www.youtube.com/watch?v=YGP_GM1bfbg

I suppose Charm-gui server is suitable for your case. http://www.charmm-gui.org/