Atoms directive missing in topology file

User discussions
1

GROMACS version:2023
GROMACS modification: No
Here post your question : After using pdb2gmx the topology file is getting generated and I am new to GROMACS. As per the tutorial I am working on, GROMACS 2022 is the software which I am supposed to work with. Since I am having a Mac M1 air, in order to use its GPU capabilities, I am using GROMACS 2023 and facing the issue where in the [atoms] is completely missing in topol.top. I have been asked to see qtot value for the protein chains in the topology file. I looked in the topology restraint file and there are many qtot values; not an overall one for the protein chain. As per the example, the value should be there. Can someone please help?

2

Could you send the commands you used and a snapshot of the error you received?

Also, would this be the ‘Lysozyme in Water’ tutorial you’re working on?

3

Tutorial running:
https://tutorials.gromacs.org/md-intro-tutorial.html

Following commands as per the link:

https://hub.gke2.mybinder.org/user/gromacs-online---intro-tutorial-2kk32w6h/notebooks/tutorial.ipynb

4

I couldn’t get the tutorial to work on binder, but when I downloaded the tutorial folder and ran the commands on jupyter lab, it seems to work fine (if someone more familiar with binder recognizes this as an issue with binder, please correct me if this is a binder specific issue).

To clarify, when you ran the pdb2gmx command (!gmx pdb2gmx -f 1fjs_protein.pdb -o 1fjs_processed.gro -water tip3p -ff “charmm27”), you found that all the atoms were missing from the topol.top file, is that correct? Are you able to open the .pdb file to check whether the missing atoms are also missing in the .pdb, or if one of the commands during the ‘Cleaning the Input Structure’ step might have been altered such that it removed more than it was supposed to?

5

There are no atoms at all in topol.top file in GROMACS 2023.

Please find the file generated below!
https://drive.google.com/file/d/1gHl3Z9YJEiAr_NcgYZ00Ar8qFKkGGXkn/view?usp=sharing

6

The atom information is right here:

; Include chain topologies
#include "topol_Protein_chain_A.itp"
#include "topol_Protein_chain_L.itp"

In the case of multiple chains, they are written to separate chain topologies, by default. This has been normal GROMACS behavior for years, so it’s not unique to version 2023.

7

Thanks, since I am new and was following the directions in the tutorial,

https://hub.gke2.mybinder.org/user/gromacs-online—intro-tutorial-w6dp5lm9/notebooks/tutorial.ipynb

Adding Ions

We now have a solvated system that contains a charged protein. The output of pdb2gmx told us that the protein has a net charge of -2e (based on its amino acid composition). If you missed this information in the pdb2gmx output, look at the last line of each [ atoms ] directive in topology file; it should read “qtot 1.” for chain A and “qtot -3.” for chain L. Since life does not exist at a net charge, we must add ions to our system. Further, we aim to approximate physiological conditions and use therefore a NaCl concentration of 0.15 M.

I asked the question.

8

The tutorial link doesn’t work for me for some reason, but it is good feedback to give the author. As someone who has spent many years crafting and refining GROMACS tutorials, the “obvious” steps are not always obvious, particularly to new users. The author is probably quite familiar with inspecting different files and it came naturally to them that one should look in the .itp files. This is not obvious at all, and worth mentioning.

9

Thanks will try to do the needful. Had the idea of asking/reporting to the team.