Aliasghar Behzadi

7 Questions 5 Answers 0 Followers

Questions related from Aliasghar Behzadi

How to dock multiple ligands with a single protein in one run?

There is a large protein that I would dock a file containing 3 different ligands with to see if distinct binding sites are filled or not. Is any software to do so? they are seemingly limited to...

30 November 2023 8,518 2 View

Is there any way to resume g_mmpbsa analysis?

I am wonder if there is a command line in order to resume g_mmpbsa analysis , as it is time consuming and such an option would be helpful heavily.

06 June 2023 7,576 1 View

What is the problem of choosing multiple options in Gromacs by echo option?

I am trying to run the command ((gmx trjconv ......)) on Google Colab. Apart from the mentioned command , there is two successive questions asking for more details after running the command. As it...

05 June 2023 3,570 1 View

How Docking can be performed on a compound protein?

When Crystallographic file of the protein contains more than 1 part , in interaction with each other while they are of two different conformer of same protein , what can be the optimal approach?...

05 April 2023 7,844 3 View

Any other way for generating .itp file of small-molecules supported by GROMOS96 43A1?

I am using GROMOS96 43A1 for MD simulation. So far I had been using PRODRG server to generate topology files of small-molecules , then reaching the mentioned server is being troublesome and not...

25 March 2023 4,833 0 View

What about setting Constraint by none and its relation with dt parameter in .mdp file of MD simulation?

Is it necessary to set none for constraint algorithm in order to provide more flexibility for protein in MD simulation ( .mdp file) ? in this case how long must be the ((dt)) parameter for each...

26 December 2022 1,862 2 View

How many steps have been processed during Molecular dynamic (MD) simulation?

Running MD simulation , NVT equilibrium, on google colab , some restarts are required due to time limitation of the server. I wonder if there is a way to find out how many steps are left to...

20 December 2022 3,148 2 View