Azam Roohi

3 Questions 4 Answers 0 Followers

Questions related from Azam Roohi

How do I generate topology of many ligands which are not coonected all of them ,for gromacs?

Hi. I want to do simulate via gromacs for ligand- protein complex which there is 9 ligands (three of them are seperated and six of them are connected together(picture in Add files). when I used...

01 January 2020 7,860 5 View

Can anyone advice how to troubleshoot segmentation fault (core dumped) during NVT equilibration stage of ligand- protein simulation?

Hi. I am using gromose 54a7 force-field and Gromacs package to simulate a protein-ligand complex.it writes pdbs for steps. Maximum force = 8.3529562e+04 But in the NVT equilibration step, the...

12 December 2019 7,302 2 View

How I can neutralize my system with counter ions, in combination with a physiological salt concentration?

I am a new Gromacs user . I want to do simulation of laccase with its ligand (N-acetyl-D-golocosamin)(NAG) which is a suger whith gromose 54a7 and I use the ATB server for production of ligand...

12 December 2019 8,835 6 View