How to restrain ligand/peptide in Protein pocket for NAMD?

09 October 2016 6,506 3 View

Anyone using NAMD for simulations?

Hello researchers I am switching from Gromacs to NAMD, i need a little help. if anyone have experience in NAMD please help me. Thanks Regards

07 August 2016 1,086 3 View

How can I find the lowest energy conformation of Protein-ligand complex after 10 ns simulation?

05 June 2016 816 9 View

What is the standard volume value in free energy of restraint?

i am calculating free energy of restraint for absolute binding free energy system of protein and ligand. i am confused between standard volume values. standard Volume is 1660A^3 , should i use...

04 May 2016 5,479 1 View

Is there any rule for selecting atoms for distance restraints?

04 May 2016 1,548 3 View

Can anyone suggest me the beginner tutorial for calculating protein protein binding free energy using GROMACS?

04 May 2016 5,134 2 View

Free energy of restraints?

03 April 2016 4,472 0 View

Volume corresponding to the one molar standard state in Gromacs?

hi gromacs experts How can i find Volume corresponding to one molar standard state. background i have Protein-ligand complex simulation and i need to find energy of restraints which requires...

03 April 2016 2,995 1 View

Can we apply simple solvation free energy calculation simulation for ligand in water simulation in absolute binding free energy calculations?

Hi, all GROMACS specialists. I have a question about ligand simulation in water. In binding free energy calculations of ligand and protein, we need two simulation systems, one -protein+ligand in...

02 March 2016 8,975 5 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 might my GFP tag be dissociating from my plasmid after transfection?

I have a set of stably transfected cell lines all transfected with plasmids containing GFP tags on the C terminus. During a western blot using anti-GFP antibody, one of my plasmids has dissociated...

01 March 2021 9,310 4 View

Precipitate after adding laemmli buffer to protein solution containing Potassium Acetate?

Hi, I am running a size exclusion chromatography experiment with a buffer containing Potassium Acetate as a salt. I analyse these fractions through SDS-PAGE. After boiling my SEC fractions in...

01 March 2021 2,622 3 View

What is the most suitable server for predicting protein structures in bacteria?

I have used the i-Tasser several times, however it has been unavailable for several days. I tried the swiss-model, but the output was not very pleasant due to the model used. Is there any other...

28 February 2021 4,521 3 View

Do you need the CMV enhancer before the CMV promotor for a proper function of CMV on the gene that follows?

I'm a student and I have to produce a cell line with a knockin for the NRF2 gene with GFP. I have to put a promotor in front of the GFP because the gene will be too far away from the promotor of...

28 February 2021 7,127 2 View

Are protein samples in SDS compatible with ELISA?

I have used an AllPrep DNA/RNA/Protein Mini Kit QIAGEN kit to extract RNA and protein from my samples. At the end of the protein purification, I resuspend my protein in 5% SDS. Will these samples...

28 February 2021 7,370 3 View

How can I calculate the rdf of water molecules around 'Na' ions that are closest(adsorbed) to the nanoparticle(solute)?

Hi, I want to calculate the radial distribution function for water molecules around the Na+ ions adsorbed on the surface of a spherical nanoparticle using the gromacs trajectory dynamically? For...

28 February 2021 5,650 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 can I assign a velocity along one direction to CO2 molecules in a molecular dynamics simulation using GROMACS?

Dear all, I am trying to perform a MD simulation about the interaction between CO2 and a polymer. I create my model, solvate it and perform the NVT and NPT equilibration. Now I am not able to...

26 February 2021 10,014 3 View

How does GROMACS calculate the average structure of proteins?

I want to get a average structure from a pdb file containing multiple models. I used the command below: gmx cluster -f input.pdb -s topol.tpr -cutoff 20 -method gromos -av GROMACS...

25 February 2021 6,314 1 View