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

Can anyone help me in understanding REMD (Replica exchange Method) protocol in gromacs?

hi Researchers and Scientists i am working on Protein ligand binding free energy, i want to use Replica exchange method for complex simulation as well as ligand in water simulation, i have studied...

04 May 2016 5,434 3 View

Is there any rule for selecting atoms for distance restraints?

04 May 2016 1,548 3 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

After a reference from Int J Body Compos Res, can any body help?

Hi, I am after the reference below, my library says it cannot obtain a copy either locally or internationally, any help appreciated! Chris Wang ZM, Heshka S, Wielopolski L, Pi-Sunyer FX, Pierson...

03 March 2021 6,193 1 View

Irradiation data for JAPAN?

Hi, Could you help me to get the latest (2019, 2020) solar resource data for a particular site in JAPAN? PV GIS and NSRDB data are not in reach to JAPAN, I'm looking for some other database for...

03 March 2021 961 3 View

Can we distinguish the type of free fluid inside the pelvic and abdominal cavities whether blood or serous fluid using the ultrasound?

during ultrasound examination of acute abdomen, sometimes we see free fluid , can we know the type of fluid ,whether blood or not , using ultrasound only? if yes , what are the sonographic...

01 March 2021 7,476 4 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

Can polymer concentrations be calculated based on the number average molecular weight?

Hello, I spin-cast two different polymers onto wafers and measure their height as a function of initial concentration. For polymer A, I have the weight-average molecular weight (Mw) as well as...

28 February 2021 7,882 2 View