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Questions related from Neha S Gandhi
I want to retain crystallographic waters in protein structure while docking a ligand. How to prepare pdbqt file in Vina considering explicit waters? Also is there any modification required in the...
05 March 2023 2,275 2 View
Is there a way-tools (Scripts) or servers that can facilitate conversion of lipid bilayers or proteins to DPD systems? How to convert coordinate and parameter/topology file to DPD?
03 January 2022 9,171 2 View
The cryo-EM structure of the spike trimer (PDB 6ZB5) is in closed conformation. I have downloaded pdb file and map (EMD_11145) files for the locked conformation. I have aligned the map of the...
13 February 2021 6,196 0 View
Selenium nanoparticles (SeNPs) have shown vital prospects in cancer medicine and nutritional science. Has anybody tried to create SeNPs from their hexagonal lattice cell and model them using...
25 December 2018 6,599 3 View
I am running a simulation of a system with 72 peptides with low hydration (not completely solvated) using AMBER MD package. The system was minimised, NVT was performed followed by NPT at 1 atm,...
28 September 2018 9,713 0 View
I want to perform docking using Swissdock. Swissdock uses CHARMM crd and psf files. I tried to build psf files using VMD autopsfgen. How can I convert pdb file from to crd format?
07 September 2018 6,875 3 View
I am running a system with protein and carbon nanotube using GROMACS 5.1.4. I used position restraints for carbon nanotube however, during NPT run (both protein and carbon nanotube fixed),it...
05 October 2017 1,505 3 View
I have seen many papers on folding and unfolding of peptides using Replica exchange with solute tempering (REST). How do we implement this method in GROMACS > 5.1?
05 June 2017 5,755 2 View
In system consisting of GOLD (Au) surface+protein+water, the gold atoms are fixed during simulation. What is the approximate density during NPT runs for such systems? Is it greater than the...
02 March 2017 3,206 1 View
I have been running protein simulations using explicit water and have been using the stepwise minimization (water first followed by solute) and then heating (NVT) followed by density equilibration...
01 March 2017 8,134 2 View
I have recently seen publications where advanced sampling methods like REMD/accelerated MD or umbrella sampling are used for loop refinement. I am particularly interested in aMD for loop...
09 December 2016 2,349 3 View
I have come across papers where protein adsorption is studied using molecular dynamics simulations on HAP 001 face. I would like to know if OH of HAP is involved in interactions with protein...
25 August 2016 8,695 2 View
Literature indicate that Calcium cannot be simply substituted by Magnesium in the hydroxylapatite (HAP) structure. The geometry (hence the packing) is different in magnesium doped HAP. Is it...
02 August 2016 4,676 5 View
The weak CH-pi hydrogen bond has currently been highlighted in biomolecules. I am interested in monitoring/calculating CH-pi interactions (if present between sidechains of aromatic residue and...
27 July 2016 9,007 3 View
I have performed PCA analyses using gmx covar and anaeig tools in GROMACS. I want to calculate the percentage and cumulative percentage of the motion explained for the eigenvectors and obtain a...
27 July 2016 3,018 4 View
I want to perform analyses on set of pdb files co-complexed with small ligands. I do not want to perform active site detection for small molecules but rather I want to concentrate on the change in...
13 May 2016 7,771 7 View
I have come across papers where Haddock was used to dock GAGs (anionic carbohydrates). What should be done if we don't the active residues/groups in the second molecule? Can we omit active...
14 March 2016 4,055 1 View
I have performed REMD simulation of a 25 residue long peptide. In advanced sampling techniques such REMD it is not recommended to plot parameters against time e.g. secondary structure along time...
20 October 2015 9,003 3 View
Is there a way/equation to calculate the adsorption energy of protein at an interface from classical molecular dynamics simulation?
01 September 2015 5,845 6 View
I have a system where the protein is embedded in water box and has a non-polar interface consisting of non-polar organic molecules such as DCE. We are trying to study adsorption of protein at the...
01 September 2015 2,069 2 View
I have 3 column data i.e. Phi, Psi (as bins) and free energy of the residue. I plotted this as a heatmap where the scale is from minimum 0 kcal/mol to maximum 8 kcal/mol. I want to calculate the...
16 July 2015 4,361 2 View
I have a polymer with a single amino acid sidechain and some linear linker groups. CD studies indicate presence of peptide like beta structures. The structure is very compact in solution as seen...
16 March 2015 1,455 6 View
I have a 1D histogram, I have binned the data, I got the frequencies corresponding to each bin. I have weighting factor/weights as well. How do I calculate free energies from weights? P.S. The...
16 February 2015 4,695 4 View
e.g amide shift of Proline in all nmr structures having sequence motif "PGSRSR"?
25 September 2014 6,696 0 View
