Manasa Surakala

4 Questions 11 Answers 0 Followers

Questions related from Manasa Surakala

How to generate pdb files of structures from GROMACS simulation results at regular intervals, say 100 ps ?

Thanks in advance. In order to check the difference between the native structure and the structures obtained from simulations, I need to get the pdb files of the latter to superimpose with the...

01 January 1970 1,541 7 View

Atomtype SDMSO not found - GROMACS?

I am new to GROMACS, running protein-ligand simulation. The error is as follows: Fatal error:Atomtype SDMSO not found. after the command: gmx grompp -f em.mdp -c solv_13948302.gro -p topol.top...

01 January 1970 6,307 5 View

Water molecule starting at atom 14394 can not be settled- GROMACS?

Thanks in advance for your help. ERROR: Water molecule starting at atom 14394 can not be settled. Check for bad contacts and/or reduce the timestep if appropriate. I tried changing mdp file and...

01 January 1970 5,098 7 View

How to plot pressure, volume and temperature graphs for protein-ligand simulations in GROMACS?

Hi, Thanks in advance for your help. I tried using the command g_energy to get xvg files that can be in turn used for plotting graphs using xmgrace but I am getting the following error: Used...

01 January 1970 6,250 8 View