Hello
Sorry, could you help me to fix the following error?
[file topol.top, line 48182]:
system has non-zero total charge: -7.000001
total charge should normally be an integer.see
Could you describe what you’re trying to do, share what commands you used and all the outputs from the commands (so copy-paste all the notes, warnings and error messages)?
Program gmx grompp, VERSION 5.1.4
Source code file: /home/student/gromacs-5.1.4/gromacs-5.1.4/src/gromacs/gmxpreprocess/toppush.c, line: 1233
Fatal error:
Atoms in the .top are not numbered consecutively from 1 (rather, atomnr = 1, while at->nr = 5052)
For more information and tips for troubleshooting, please check the GROMACS
website at Common Errors — GROMACS webpage https://www.gromacs.org documentation
It seems the atoms in your .top need to be numbered consecutively from 1, you’ll have to figure out what might have gone wrong when you made the .top file
The protein is a homology model, can this be the reason for the error?
Did that affect how you generated the topology file? The second error you sent is an issue with how the atoms were numbered in the file, not with the structure itself. The first error is harder to diagnose without more information on your forcefield, what commands you used, how you set the system up, additional messages that were output from the command, etc. You also seem to be using an older version of gromacs, and it’s possible there are bugs associated with the version that I’m not familiar with.
Thank you
Were you able to resolve this? can you kindly say how? I am currently facing the same error while trying for CG simulation