02 February 2016 1 3K Report

Hello, I want to represent some protein structures with vectors? 

Thank you,

Mijiddorj

More Batsaikhan Mijiddorj's questions See All
Why does npt equilibration generate free space ?

During the nvt it was okay. After the NVT equilibration, short NPT equilibration was performed. During this equilibration, free space generated inside box. Please tell me some possible reasons?

09 October 2018 8,681 0 View

How to estimate hydrophobic interactions and electrostatic interactions between the protein chains using GROMACS?

Dear GMX experts, A simulation system consists of several peptide chains, and I would like to compare contacts of hydrophobic and electrostatic interaction. How can I estimate hydrophobic...

03 April 2018 9,973 3 View

How to convert CHARMM .str to .itp file for GROMACS?

Dear Experts, I generated LIG.str file using CGenFF for a specific molecule. I would like to use GROMACS package. I tried to convert LIG.str file to LIG.itp file. I tried as following command...

31 December 2017 9,559 3 View

How can I know the structure was optimized or not?

Hello, I am very new user of Gaussian. I started the optimization of the connected two amino acids. Calculation was finished, and I would like to get the optimized structure. How can I know...

05 June 2017 7,247 5 View

Can someone verify my singular value decomposition of 3D helical data?

Dear all, Hello, I have a 3D helical data consist of  40 points. I calculated SVD() using matlab, and I have got values (110, 10, 10). I understood that 110 is a dimension of the most variation...

01 February 2016 8,496 0 View

How do I make a pH dependent simulation of Oligomer structures?

Hello, I want to make pH dependent simulation of dimer, trimer and pentamer structure of peptide. How to make it using AMBER or GROMACS? Can I use H++ server for oligomers? or How to set manually....

31 December 2015 910 2 View

How to fix malloc error during MM-PBSA calculation on AMBER14

Hello, I have got following error during MMPBSA.py calculation for PBSA MD simulation. How to fix it? ******************************************************************** Beginning GB calculations...

10 November 2015 10,207 2 View

Similar questions and discussions
GC-MS retention index prediticon?

Hello experts, Does anyone know any free software about retention index prediction ?

08 August 2024 7,403 2 View

Gromacs first step of minimization ?

I have face this problem anyone help me how to solve this issue ?which is below Fatal error: There are inconsistent shifts over periodic boundaries in a molecule type consisting of 78 atoms. The...

07 August 2024 2,598 1 View

Are there instances where molecules with larger molecular weights exhibit greater mobility than those with smaller molecular weights?

Hi, I know that low molecular weight (MW) molecules generally tend to have higher mobility, while high molecular weight molecules tend to have lower mobility. However, in my experimental...

06 August 2024 1,495 2 View

Weak DAPI staining after immunohistochemistry - how to improve?

After immunohistochemistry of previously fixed in PFA and EtOH and then frozen 20 μm sections of zebrafish brain, DAPI staining is very weak (right) compared to the same sections stained without...

05 August 2024 9,637 2 View

Why did the authors extrapolate a phenotype that they experimentally proved in one bacterial strain across the whole genus of the organism?

I aim to be as skeptical as possible regarding whether a pair of orthologous genes results in the same phenotype in their different but related bacterial organisms under similar environmental...

05 August 2024 6,787 4 View

The Curse of Evolution and Complexity?

Brain and body mass together are positively correlated with lifespan (Hofman 1993). The duration of neural development is one of the best predictors of brain size, and conception is the best...

05 August 2024 6,247 3 View

For an in-vitro drug release study, what molecular weight cut-off (MWCO) dialysis bag is required for a 117 kDa protein?

kindly reply me. Thanking you in advance.

05 August 2024 7,727 4 View

How to start a Molecular Dynamics Simulation?

Is it possible to conduct a molecular dynamics simulation to see the effects of a specific carbohydrate on the structure of lipids (e.g., micelle structure)? I am a beginner in this field and plan...

03 August 2024 3,371 3 View

Which will be the best software for the Hydration shell analysis with molecular dynamics?

I am using a windows system, what software I should use for hydration shell analysis with molecular dynamics?

02 August 2024 3,143 4 View

Can anyone provide me with molecular docking softwares/ websites?

Molecular docking software/ websites?

02 August 2024 8,704 7 View

Our partners will collect data and use cookies for ad personalization and measurement. Learn how we and our ad partner Google, collect and use data. Agree & close