Yogeshwar Vikram Dhar

6 Questions 7 Answers 0 Followers

Questions related from Yogeshwar Vikram Dhar

Molecular Dynamics of Arsenic ligand with protein?

Dear all, i am working on analysis of protein-ligand interaction by molecular dynamics. My ligand of interest is disodium arsenate, to run MD with this ligand i need its .itp file but not able to...

10 October 2017 9,151 2 View

Problem in adding other molecule in system for molecular dynamics

Hello all, i am working on a protein complex. For a certain analysis, i am trying to add ethylene molecule in system (Protein + water), to check the variation in system. I have inserted 10...

07 July 2017 8,657 4 View

Gromacs error while mdrun

Hello all, i am working on a protein complex. I have opted simulation analysis for some specific analysis of my complex. For which i have generated a system for complex in water having 10...

06 June 2017 6,370 0 View

How to define option in g_rms in PBS file

Hello everyone, i am working on gromacs tool (V 4.6.5). Server, in which we work, accepts PBS for job runs. I have prepared my .tpr file on local machine and performed the mdun on server. As my...

05 May 2017 8,601 12 View

I am working on DNA-protein complex MD in gromacs, how ever stuck on a step where in grompp step getting 'Fatal error: No such moleculetype DNA' ?

I am interested in DNA-protein MD. I have a custom made structure of a DNA motif, i have edited it (from ATGC to DA, DT, DG, DC) for gromacs and generated topology using amber99sb-ildn.ff. After...

02 February 2017 1,859 5 View

i want to use simbiology feature of MATLAB software for system biology simulation ...but have no idea about filling the compartments of it and the RUN...

i want to use simbiology feature of MATLAB software for system biology simulation ...but have no idea about filling the compartments of it and the RUN(simulating) the model programming.... please...

09 September 2011 5,086 0 View