I'm building a psf for Xplor, I use LTOD patch to change L-proline to D in a peptide, but when I visualize the structure in VMD, the rings of PHE and TYR deform...That is absurd, because the patch don't act in those aa...
I want to obtain the NMR structure of a synthetic peptide using Xplor-NIH. The compound has a residue that does not appear in the FF of the Xplor-NIH and I am interested in parametrizing it....
09 October 2018 1,826 1 View
annealtt.py(48): protocol.genExtendedStructure() fixupCovalentGeom: Covalent geometry still violated at exit. ........ As a result, some angles and dihedrals are violated, and structures are not...
08 September 2018 8,613 0 View
We are doing a molecular dynamic simulation with GROMACS using the AMBER force field. During the simulation the disulfide bonds are increasing over time. We set the bridge manually with pdb2gmx...
05 June 2015 5,706 3 View
We intend to study the interaction between peptides and polymer (like PP, PE and PS) through MD simulations using Martini force fields ( Martini 2 for PP and Martini 3 for PE, PS). We have...
08 August 2024 4,842 0 View
Hi, I'm currently working on a project where I need to plot the atom-projected band structure using GPAW. I've been able to calculate the band structure for my material, but I'm having trouble...
07 August 2024 269 3 View
Visual Studio Code (VS Code) has become a popular choice among developers for several reasons: 1. **Free and Open Source**: VS Code is free to use and open source, making it accessible to...
07 August 2024 7,013 4 View
Hi, we have measured tryptic peptides using both DDA and DIA method on QExactive. In DDA replicates i saw unusual intensity drops occurring at the same sections of chromatograms in DDA replicates...
07 August 2024 3,218 4 View
I have protein-membrane simulations (PDB, PSF, DCD) and have noticed that water molecules near the protein are not visible in the simulations. How can I fix this issue? Is there a way to place the...
04 August 2024 1,200 2 View
Hello, I am currently analyzing some phosphoproteomics data, but I have peptides with multiple phosphorylation sites or phosphorylations together with carbamidomethylation or oxidation. How can I...
04 August 2024 8,432 3 View
Recently I'm trying to use Sep-pack C18 1 cc Vac Cartridge (Waters: SKU: WAT054955) to desalt digested peptides. However, the recovery rate is usually 40-60%. What is the normal recovery rate?
31 July 2024 6,544 11 View
Hi all, My lab has Thermo Scientific™ Invitrogen™ EVOS™ FL Auto 2 Imaging System, and I was wondering if I will be able to use it with whole blood, whilst focusing on platelets? The idea would...
24 July 2024 9,337 3 View
Hello, I am searching for the binding position of a drug in a ribosome, based on previous work indicating it binds there. The resolution of the ribosome-drug Cryo-EM map is around 2.5 Å. I've been...
19 July 2024 2,155 0 View
So i have a few peptides (synthesized by SPPS and not cleaved from resin) and I want to add a maleimide label. We have NHS-PEG-Maleimide and from literature it is evident that the free amine group...
18 July 2024 4,075 3 View