Problem with Introduction to Molecular Dynamics tutorial

User discussions
1

I am new to MD and to Jupyter, so started at square one with the Intro to MD tutorial. Everything went fine until the step for assembling the .tpr file. I got the following error message:
Fatal error:
number of coordinates in coordinate file (1fjs_solv.gro, 39748)
does not match topology (topol.top, 75079)

I didn’t notice this error until I tried the next step, which was to pass the .tpr file to gmx genion, and got the message that it failed because it couldn’t find the .tpr file:
Error in user input:
Invalid command-line options
In command-line option -s
File ‘ions.tpr’ 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)

Have others experienced this problem? I did not make any changes as I went through the tutorial, simply ran each step in succession, so it seems to me there is a problem somewhere in the coding of the tutorial.
Thanks in advance for any help you can offer!

2

Hello there,
it’s probably due to misplace of your “.itp” file in topology file read generating topology section in Gromacs tutorial an check if you have inserted “.itp” file in correct places( i’ll give you a hint to find it in tutorial:
; Include Position restraint file
#ifdef POSRES
#include “posre.itp”
#endif

; Include ligand topology
#include “jz4.itp”

I wish it would help you.

3

There is a mismatch in the coordinate numbers. Did you update the topology after the addition of water?

1 Like
4

Did you run the solvate step twice? If so, the end of your topology file should look like this:

[ molecules ]
; Compound        #mols
Protein_chain_A     1
Protein_chain_L     1
SOL             11777
SOL             11777

gmx solvate did not regenerate the whole topology file, but just added to it and that’s why you got a mismatch in the number of atoms. If you remove the extra SOL-line, it should work. You can remove the last line from the topology file directly in the Jupyter notebook by opening a new cell somewhere between gmx solvate and gmx grompp and pasting the following command (but just run it once! :) ):

!head -n -1 topol.top > temp.top ; mv temp.top topol.top
5

Thanks, all, for the helpful suggestions! Not sure what I did wrong the first time, but the tutorial worked for me on the 2nd try.