Divya Jhinjharia

4 Questions 3 Answers 0 Followers

Questions related from Divya Jhinjharia

What does the "Failed to kekulize aromatic bonds in OBMol::PerceiveBondOrders" error mean in galaxy-europe?

Good afternoon everyone, Looking for an explaination for the error : Open Babel Warning in PerceiveBondOrders Failed to kekulize aromatic bonds in OBMol::PerceiveBondOrders while performing...

27 March 2023 2,107 0 View

Can we change the time from ps to ns in gromacs to analyse energy curve?

Hello everyone! Can anyone please help me out in plotting an energy graph in gromacs, the problem is that I've simulated my system for 1 microsecond and since at every 2 pico second the output is...

11 May 2022 1,983 4 View

Fatal error: Syntax error - File ffnonbonded.itp, line 1 Last line read: '[ atomtypes ]' Invalid order for directive atomtypes?

Even after including all the forcefields in the topology file still facing this issue. I am attaching the files supporting. Complex is intact with ligand but while adding ions : gmx grompp -f...

06 April 2022 2,781 1 View

Can anyone please guide me through carrying out simulation of a larger membrane protein system, is there way to simulate a specific region ?

In gromacs while performing membrane protein simulations, it is taking much time to complete mdrun step as the protein system is huge, so I want to ask, is there a procedure which can be...

21 December 2021 1,749 2 View