How to optimize geometry of nanoparticle for docking?

Hello Folks, I want to dock nano-particle like Fe2O3 in protein. I need to optimize the geometry of such nano-particle structure. Is there any online approach to assign partial charge and...

31 December 2017 6,374 6 View

How to explain the WHATCHECK out put of SAVES Validation server?

Hello everyone,Previously, i asked a question regarding SAVES validation server (https://services.mbi.ucla.edu/SAVES/),I want to extend that question again. I could not understand why the output...

05 June 2017 5,517 0 View

How to elaborate SAVES Server output results?

04 May 2017 3,427 0 View

What's the difference between the I-TASSER and LOMETS?

Hello dear members, I want to build homology model for my target protein while using online server where the algorithm should be based on threading, because the available templates from PDB for my...

01 February 2017 1,623 2 View

Should i restraint protein and ligand in md production?

Hello folks, I want to conduct md simulation to explore the comparative stability and interaction mechanism of the reference compound (experimentally determined) and the newly screened candidate...

01 February 2017 9,253 4 View

What's the basic criteria to select a suitable forcefield for protein-ligand complex MD simulation in gromacs?

Hello, I want to simulate my protein-lignad complex, but there is no forcefield information cited yet for this specific protein. I'm seeking the basic criteria which is taking in consideration to...

10 November 2016 933 9 View

Is there any hard and fast range for NVT and NPT to decide whether our system is equilibrated or not?

Hello, I prepared my protein-ligand complex for MD run, the average value for NVT is 299.99 which looks pretty satisfactory, but for NPT, the average value is 10.01 which is strange to me. I...

10 November 2016 2,384 7 View

Hello, How may we merge the .itp files contents when we using Amber force field in gromacs?

Hello, I have generated ligand's topology files through acpype, the number of ligands are two. when we want to run simulation on gromacs, we gonna merging the two files especially their atomtype...

09 October 2016 4,798 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 almost every element would be metallized in sufficiently high pressure and low temperature?

(This statement is from wikipedia, BTW). What is so special about metallic bond that is limiting high-P low-T state of a matter (as long as individual atoms exist, not white dwarf of neutron star...

02 March 2021 3,309 2 View

What is the difference between genotype and haplotype data in the ped format?

Hi everybody In the ped format for genotype, alleles of any SNP are represented by two columns (one for each allele, separated by a space). Is a column sufficient for the haplotype to...

27 February 2021 1,965 1 View

How to calculate Ligand-active site distance in a ligand-protein complex from MD simulation?

I have run a MD simulation of a ligand-protein complex in GROMACS using CHARMM forcefield. Reviewer has asked me to calculate Ligand-activesite distance and binding free energy of ligand with...

27 February 2021 4,703 1 View

How to formulate Energy minimization in Molecular dynamics simulation for alloys using meam potential?

during MD simulation, the atoms are not moving as per required. The problem (as per my observation) lies in energy minimization technique. upon application of tensile strain in x or y direction,...

22 February 2021 380 5 View

Are there any databases for gene co-expression or expression pattern clustering?

I am currently working on gene clustering based on co-expression pattern in mouse brain. The problem is I do not have some solid way to test my result. Are there any suggestions for databases...

22 February 2021 4,374 3 View

Magnetismic Gravity in the universe?

MAGNETISMIC GRAVITY What is magnetism? Something magnetic has a + and - charge. If 2 + or - are pushed if + and - are pulled. But what is the main reason for this? Why does magnetism have a pull...

21 February 2021 9,538 3 View

Has anyone succeeded in capturing uranium atoms in a fullerene structure?

Additional questions are: What are the encapsulating atoms? How difficult was the process and what rates were achieved? What factors most seriously affect the economics?

20 February 2021 3,134 5 View

How to get the vector of a specific vibration mode in phonon dispersion?

For example, I have this phonon dispersion(Fig. 1), and now I would like get vector of atoms which describes TA1 in P. I know v_sim can show vibrational animation of specific mode, but I do not...

20 February 2021 4,332 4 View

What are the potential shell well and atomic solvation parameters for the boron atom?

I have a protein-ligand docking project. The ligand contains boron atoms that are not detected by Autodock software. To solve this problem, it is necessary to introduce the boron atom to...

19 February 2021 1,236 1 View