Ammar Danazumi

3 Questions 6 Answers 0 Followers

Questions related from Ammar Danazumi

Parameterisation of Metallo-protein with amber?

Can someone please help me with a protocol for parameterizing a metallo-protein for MD simulation with amber forcefield? My protein has two FE molecules and the I tried using either...

20 April 2022 4,459 1 View

How to troubleshoot SLIC reaction?

Please can anyone offer a suggestion on how to trouble my SLIC reaction? I am trying to clone two short constructs of my protein (120bp~35aa), one of the constructs appears to be cloned but the...

04 April 2021 8,907 1 View

GROMACS: Cannot rename checkpoint file; maybe you are out of disk space?

Hi! i am running a simulation using a cluster and I have encounter an error during my nvt equilibration like this: Cannot rename checkpoint file; maybe you are out of disk space? I deleted some...

04 January 2021 3,941 2 View