Mahboobeh Azarakhsh

6 Questions 14 Answers 0 Followers

Questions related from Mahboobeh Azarakhsh

Fatal error: Atom type OUrea (residue UREA) not found in atomtype database??

I am running the pdb2gmx command for my protein using Gromos 54a7 force field, but I have this error: Fatal error: Atom type OUrea (residue UREA) not found in atomtype database while this atom...

05 May 2023 133 2 View

Apply post translational modification in pdb file before MD simulation?

I am going to calculate the binding energy between two proteins, which one of them is post translationally modificated. Is there any way to apply this PTM in pdb file before MD simulation?

19 January 2023 3,712 3 View

Error while calculating binding energy using gmx_mmpbsa?

I am trying to calculate binding energy between two protein using gmx_mmpbsa, but when I am running the last command to calculate binding energy (gmx_MMPBSA -O -i mmpbsa.in -cs md.tpr -ci...

10 June 2022 3,118 6 View

Is it possible to use such RMSD graph for publications?

I ran a simulation for two proteins in a complex, but the RMSD graph show instability after 45 ns. is it possible to represent such RMSD graph in article or use it for analysis?

23 May 2022 6,120 0 View

The two protein do not separate completely during umbrella sampling!?

I am going to calculate the free binding energy of two proteins which are in a complex. I have used the umbrella sampling for this purpose, but after pulling, the two proteins do not separate...

07 March 2022 2,041 5 View

Calculating free binding energy between two proteins using umbrella sampling?

Hello, I am going to calculate the free binding energy between two proteins using umbrella sampling. I have docked the two proteins in a complex and then fixed one of them and pulled another...

11 February 2022 4,984 12 View