GROMACS version: 5.1.1
GROMACS modification: Yes/No
Hello. I am working on protein-ligand MD, but I am facing difficulties in making the complex.gro. I initially made the mistake of not increasing my atom count on the second line of my complex.gro file, so I got the bad box warning. I then made the necessary corrections and included the additional ligand atoms to the count. I am now getting this error:
Fatal error:
Something is wrong in the coordinate formatting of file 1bkn5b.gro. Note that gro is fixed format (see the manual)
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
My complex.gro file looks like this:
Gyas ROwers Mature At Cryogenic Speed
5456
20VAL N 1 9.505 6.917 8.459
20VAL H1 2 9.524 6.917 8.361
.
.
.
1FB5b H 46 25.715 21.334 -0.014
1FB5b H 47 25.908 21.451 0.104
1FB5b H 48 26.224 20.779 -0.018
8.13590 9.16000 6.11230
the error message concerns the file formatting, which is impossible to see in your posted message since that removes the formatting. Could you upload the file somewhere, or post the snippet inside a code block?
Hi,
pls how did your eventual solve this problem:
Fatal error:
Something is wrong in the coordinate formatting of file complex.gro. Note that
gro is fixed format (see the manual)
