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Hi to all,
I have this error when I try to run the command gmx grompp -f em.mdp -c solvions.gro -p topol.top -o em.tpr
Warning: atom name 54579 in topol.top and solvions.gro does not match (Cal - CA)
Warning: atom name 54580 in topol.top and solvions.gro does not match (Cal - CA)
Warning: atom name 54581 in topol.top and solvions.gro does not match (Cal - CA)
Warning: atom name 54582 in topol.top and solvions.gro does not match (Cal - CA)
Warning: atom name 54583 in topol.top and solvions.gro does not match (Cal - CA)
Warning: atom name 54584 in topol.top and solvions.gro does not match (Cal - CA)
Warning: atom name 54585 in topol.top and solvions.gro does not match (Cal - CA)
Warning: atom name 54586 in topol.top and solvions.gro does not match (Cal - CA)
Warning: atom name 54587 in topol.top and solvions.gro does not match (Cal - CA)
Warning: atom name 54588 in topol.top and solvions.gro does not match (Cal - CA)
Warning: atom name 54589 in topol.top and solvions.gro does not match (Cal - CA)
Warning: atom name 54590 in topol.top and solvions.gro does not match (Cal - CA)
Warning: atom name 54591 in topol.top and solvions.gro does not match (Cal - CA)
Warning: atom name 54592 in topol.top and solvions.gro does not match (Cal - CA)
WARNING 2 [file topol.top, line 43875]:
14 non-matching atom names
atom names from topol.top will be used
atom names from solvions.gro will be ignored
I already check the topology file and coordinate file if ever the sequence of atoms are not the same. The error is still the same. What should I do?
Thank you.
Hi,
the problem is not the order but the atom name used in the topol.top and in gro.
In one file the calcium is named ‘Cal’ and in the other file is named CA.
If you are sure that the correspondance between Cal and CA is correct, you can ignore the warning, but be aware that only atom names from the topol file will be used for the output.
Best regards
Alessandra
Thank you for your response. I fix this problem but there are some notes and warning when I run energy minimization. Here is the image of warning and notes. Hoping for your help. Thank you.
Hi,
your system is charged +29 and as the warning (WARNING 1) explains that can lead to problems.
When you add ions to the system (gmx genion) you can use the option [ -neutral ] to ensure that you neutralize the system. You can use it together with - [ -conc ] to control also the ions concentration
See more on gmx genion here (gmx genion — GROMACS 2021 documentation)
Regards
Alessandra
Hi, I already do that, -neutral and -conc at the same time in gmx genion, but the warning still appears.
Hi,
Did you get any warning from gmx genion?
Can you provide the command you use for gmx genion?
Thank you
Alessandra
No, I don’t get any warning from genion, the warning appears in gmx grompp in energy minimization.
Here’s the command i use in adding ions:
gmx genion -s ions.tpr -o solvions.gro -p topol.top -pname CA -nname CL -conc 0.03 -neutral
Hi,
I guess the problem is that gmx genion has as default +1 for positive ions, while CA is +2. Thus the tool does not properly add ions to neutralize the system.
You can run gmx genion using (in adding) the option -pq 2 to specify the charge of positive ions.
Best regards
Alessandra
Hi Alessandra, Thank you very much, I follow your instructions and it worked. Thank you.
