13 Questions 26 Answers 0 Followers
Questions related from Mahesh Kumar Velusamy
Dear All, Recently, we have used cgenff Parachem web server "https://cgenff.paramchem.org/" to generate parameters for glucosylated aspartyl residue that exist in high energy non-native sugar (x)...
03 March 2018 5,013 1 View
I am trying to run simulation of a glucosylated residue which covalently interact with aspartate. During validation of topology and preparation of energy minimization (EM) step (grompp) I am...
02 February 2018 9,788 8 View
Dear All, We are working on parametrization of x non-standard (NR) residue using Charmm22, GLYCAM 06 (amber format) and GAFF force fields. Among these, we can able to parametrize them...
10 October 2017 8,775 3 View
In a case where we carried out a genetic Screening of genes that involved in the stress response in E. coli. From this screen we identified a gene that encodes a 50 kDa flexible protein (Protein...
11 November 2016 7,468 4 View
Hi All, I have a protein model with covalent bond (ASP + B-D-GLUCOSE) and i am trying to do energy minimization on it by using gromacs with amber99sb force field but since my model has covalent...
08 August 2016 846 0 View
Dear All, I have tried to build topology file for a structure that has covalent bond (Between ligand and protein) by using pdb2gmx with the following command: pdb2gmx -f WILD0MODEL.B99990001.pdb...
08 August 2016 7,002 7 View
Dear All, I have tried to generates models for single point mutation along withown optimization and refinement criteria on the selected region of atomsaround the mutated residue which works fine...
07 July 2016 4,333 2 View
Dear All, I hope you all know that default mutate_model.py script works only for single mutation but I want to make it for double and combination of mutation and I beleive this would be possible...
06 June 2016 3,362 1 View
I hope you all know that there is script available in modeller "mutate_model.py". To generate a mutant models and then optimize the mutated residue following refinement in sidechain alone but I...
06 June 2016 2,779 4 View
Hi All, I am looking for the best bionformatics tool to predict the protein stability changes upon mutation and I found that there is many tools avail for the same here...
05 May 2016 3,837 6 View
I am very new to MPI version of autodock4 and I didn't find any good resource to learn how to do MPI version of autodock4. So If anyone knows the good resource with an example could you suggest me...
07 July 2015 7,123 0 View
I tried docking an enzyme which is randomly mutated in order to improve the catalytic efficiency. Then tried to find best catalytic efficiency among all the mutated versions of the same enzyme...
05 May 2015 7,157 14 View
I am using NADH as a ligand for my docking which has puckered ring. Since CDOCKER force field (charm) considers a full ligand as flexible, I am getting the docked ligand posed with a flat ring...
04 April 2014 749 0 View
