21 Questions 32 Answers 0 Followers
Questions related from Rohit Shukla
Dear researcher, I want to simulate my protein with the denaturants (MW-139 Da). I am using Gromacs 2018.2 version and the extra molecules were added by using gmx insert-molecule command. I want...
02 February 2019 1,557 3 View
Dear researcher, I want to simulate my protein in different concentrations of Guanidinium chloride. I successfully added 4M GdnHCl in a cubic box. But when i want to neutrilize the system with the...
11 November 2017 9,135 0 View
Dear researcher, I want to simulate a protein-DNA complex. I can simulate the whole DNA but i want to simulate the nicked DNA. When i try to generate the topology of...
11 November 2017 4,328 0 View
Dear researcher, I want to simulate a selenium containing enzyme. But when i processed the selenium containing enzyme using pdb2gmx command so it is showing an...
10 October 2017 6,191 11 View
Dear researcher, I want to generate a free energy landscape using Essential dynamics analysis. I calculated a free energy landscape using g_sham tool. But it is not...
06 June 2017 4,790 5 View
Dear researcher, I did the molecular dynamic simulation of a protein till 50 ns. My protein got the equillibriation state after 10 ns. I took the last 10 ns trajectory...
03 March 2017 7,473 6 View
Dear researcher, I am working on molecular dynamics simulation. I did the MDS of protein ligand complex. Currently i am working on urea induced denaturation of...
02 February 2017 7,909 4 View
Dear researcher, I have calculated mm-pbsa for protein ligand complex. I considered only last 5 ns trajectory then i found these values. van der Waal energy = -151.712...
12 December 2016 5,765 6 View
Dear researcher I did a molecular dynamic simulation of wt and mutant protein. Till 10 ns the structure is stable but after 10 ns the mutant diamer is dissociated. I...
11 November 2016 8,508 5 View
Dear researcher, I want to calculate the dynamic cross correlation map for a WT and mutant protein. Can i use the covariance matrix as correlation map, which is...
11 November 2016 7,229 0 View
Dear researcher I am facing a problem in principle component analysis. I calculated the eigenvalue by g_covar command. After that i saw in many Literaturrates they give the percent value. In...
10 October 2016 4,805 4 View
Dear researcher, I am a learner of Gromacs. I want to simulate my protein in different pH. in .mdp file i did not saw any option to define the pH. please suggest me how...
10 October 2016 9,742 5 View
Dear researcher, I did the molecular dynamic simulation of native protein. I am working on protein folding. I want to add the urea molecules in Gromacs. How to calculate the number of urea...
10 October 2016 8,521 9 View
Dear researcher I have docked a compound with enzyme. It gives -5.4 Kcal/mol binding energy. Complex was stabilized by 5 Hydrogen bonds and many hydrophobic interaction....
10 October 2016 6,387 5 View
Dear researcher, I did a protein ligand Molecular Dynamic simulation and protein MDS for 50 ns both. In the Protein simulation, the RMSD is stable till 50ns. But when i add the...
07 July 2016 3,563 6 View
06 June 2016 7,223 4 View
Dear all, I generate the ligand topology using Swiss-Param server. I generates the protein topology using Charmm 27 forcefield in Gromacs. When i am doing the Molecular Dynamics...
02 February 2016 7,075 1 View
I want to proceed high throughput screening of my protein. Since we don't have any subscribed softwares for HTS, kindly provide the tools for free HTS for academic use. Thanks in advance
01 January 2016 3,850 6 View
Dear all, I want to do a molecular dynamic simulation of Amino-acyl t-RNA synthatase enzyme with its substrate ATP, AMP and t-RNA. So please suggest me which force field is best for...
01 January 2016 5,775 5 View
Dear all, I want to do a molecular dynamic simulation using Charmm27 force field in gromacs. I generate the ligand topology by http://www.swissparam.ch server. It takes .mol2 file as...
01 January 2016 2,193 2 View
Dear all, 1- I download the g_correlation_1_0_2_tar.gz file from http://www.mpibpc.mpg.de/grubmueller/g_correlation. 2- I unzip that file, so i found a installation instruction file and make file...
12 December 2015 6,404 5 View
