Molecular Dynamic(MD) CYP3A4 Structure

I am Samuel I am using for MD of CYP3A4 structure but I could not pull through the problem started from the Merge Gromacs.

However I’m using this as the TEMPLATE:

Kindly assist

Hi Samuel,

can you ensure you are using version 3.2.0 of the ‘Merge topologies’ tool? You can specify the version by clicking ‘Versions’ at the top of the central panel.

If this doesn’t help, please provide exact details of your error and I can try and help.

All the best,


Hello Simon,

I really appreciate your assistance and it works. I was able to overcome the energy minimization steps.

However on getting to the Equilibration stage I got errors (NVT/NPT).

I have some questions to ask for clarification on my CYP3A4 MD modelling which has 2 Ligands (Z9Z and HEM) compared to HSP90 which has one in the Template I am using. This I encounter at the search textfiles level.

I will be glad to have a breakthrough using this Galaxy tool for my CYP450 enzymes for my MD.

I will be glad to share my history with you.

Thank you.

Best regards,

Hi Simon,

I am very sorry to border you.

In the course of looking through the GROMACS NVT equilibration I discovered that at the Number of Steps for NVT which was 50000 was written on the GROMACS NVT equilibration as NPT.

I want to be sure that this is not a mix up and causing the errors I am seeing.

Thank you for always being there.

Best regards,

I missed this last comment, sorry. Yes, this is an error in the tool. It needs to be fixed.

It shouldn’t make a difference to any errors you are seeing though.

All the best,


Dear Simon,

Thank you Simon.

I will be very happy to see the Equilibration stage tool fixed.

And with respect to the Ligands I await your opinion on how to go about it.
What infers the search textfiles of the Ligands to match either one or two Ligands?

Thank you.

Best regards