I want to take the pdb file of ligand-receptor complex for MD simulation in GROMACS.
I did MD simulation for 10 ns. the ligand was inside the simulation box upto 10ns. only in the 3rd ns the structure was ok. in all other time one of its double bond was missing. many times the OH...
11 December 2015 3,695 7 View
How can I convert an enzyme pdb file into a topology file for GROMACS use? Note that I don't have the facility to run GROMACS. I have to use its webportal. PRODRG converts only ligands into...
05 June 2014 3,813 2 View
I have been doing the m6A dot blot for a while with no improvement, I am extracting the RNA, and I can see the dots although the three biological replicas give a different reading on the memberan...
10 August 2024 8,539 5 View
How can I use the cif data obtained from rietveld refinement extracted via gsas2, for microstructural analysis using ETEX software?
09 August 2024 7,718 0 View
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
Palmitic acid presence in aqueous fraction
05 August 2024 8,624 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
I work on MCF7 cell cell for anticaner purpose and I wa to do drug preperation the drug ( secondary metabolites extracted from Aspergillus) My question which solvent is better with these secodary...
03 August 2024 4,725 2 View
Molecular docking software/ websites?
02 August 2024 8,704 7 View
I am conducting a systematic review and meta analysis; as I am extracting data I realized there is a consort diagram that shows the number of patients from randomization till end of the study. So...
01 August 2024 9,993 3 View
99% pure ethanol was used for maceration also alternate methods along with the temperature and time to concentrate the extract can be specified
31 July 2024 5,113 4 View
We conducted an antibacterial study of a plant extract. Varying concentrations of crude extract were subjected to microbroth dilution assay. The result showed that only the lowest concentration of...
31 July 2024 8,666 3 View