How can I extract one chain from a dimer receptor and repairing the missing atom after that to prepare it for molecular dynamic simulation?

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Abaqus effectiveness proven ?

hello dear scholars , i am looking for papers proving if abacus has failed crack growth simulation of bonded joints or delamination in composite structures? my question is concerning the...

06 August 2020 7,852 1 View

Why are two (non-RNA) bands appearing in my 1% agarose gel of gDNA?

I carried out DNA extraction from skin biopsies of warts using Qiagen's QIAamp DNA Mini Kit. I performed off-column RNase digestion followed by ethanol precipitation.

07 May 2018 9,328 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

16 June 2021 0 0 View

fatal error

16 June 2021 0 0 View

fatal error

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

Indu Kumari

Monomer can be obtained by selecting the residues of either chain A/B (preferably the chain which is involved in the catalysis) using PyMOL and then save the selected residues by using the option SAVE MOLECULE. The missing residues can be added to the monomer using SwissPDBviewer.

Amneh Shtaiwi

Thank you for reply, I will see the SwissPDB viewer software, Is it free download?

Yes, it is available freely to download.

Thank you.

Robert P Bywater

Use YASARA. It will do all that for you and also enable you to run MD in lipid bilayer..