GROMACS version: 2021
GROMACS modification: Yes/No
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While performing protein-ligand interaction I encountered this fatal error saying that my coordinate numbers in coordinate file did not match the topology file. so please help me to resolve this error mentioned below:
Program: gmx grompp, version 2020.1-Ubuntu-2020.1-1
Source file: src/gromacs/gmxpreprocess/grompp.cpp (line 669)
number of coordinates in coordinate file (solv.gro, 33508)
does not match topology (topol.top, 33509)
the error is as the message says: your topology file (
topol.top) has 1 more atom than your coordinate file (
solv.gro). You need to correct either file to make them match.
Thanks a lot, but will you please tell me how to match this number?
How many atoms are in your ligand in its topology vs. its coordinates? Most often, a difference of one atom is a result of using coordinates that have a different protonation state than the topology.
22 atoms are their in my ligand. Rest am new to Gromacs so I dnt know how to differentiate between these two files and make them to have same number of atoms?
Initially when the error appeared the number of coordinates in solv.gro file is 33508 and topol.top file is having 33530 number of atoms but somehow with the help of google searches and responses I reduced the topol.top file error from 33530 to 33509. But now the remaining 1 atom differnce is not reducing and hence both the files remain unmatchable with equal number of atoms. So here am looking for any suggestion that how to reduce this one atom error and make them equal in both the files.
You need to provide exact, step-by-step descriptions (including actual commands, where relevant) as to what you did. There are too many things you might have done that were right or wrong for us to tell. You also did not directly answer my question about about ligand atoms - 22 in coordinates or topology? What did you do to “solve” the original discrepancy in terms of the number of atoms? There shouldn’t be too much magic that is ever necessary here, and rectifying this mismatch issue is always the same solution - let tools like
genion update your topology for you in terms of water and ions, do not make manual edits to those numbers, and carefully copy and paste ligand coordinates and update the topology accordinatly.
If you need further help, please provide the exact details I’ve noted above. Without that, it’s just unproductive guesswork.
okay let me just go through it again and then tell you about it sir. Thanks a lot sir.
Sir by your help am able to resolve the issue; thank you. But in upcoming step ’ Equillibration - Thermostats step" I have encountered another error while running the command “gmx make_ndx -f em.gro -o index.ndx”
i.e. as follows-
Error in user input:
Invalid command-line options
In command-line option -f
File ‘em.gro’ does not exist or is not accessible.
The file could not be opened.
Reason: No such file or directory
(call to fopen() returned error code 2)
Please advise me how to overcome this error and also from where did this em.gro file will be found?
Hope to hear soon.
Thanks in advance sir.
That means your previous step (presumably energy minimization based on “em” as the file name) failed. Pay attention to warnings and errors printed to the terminal and output files.
okay sir,will do the steps again carefully.