GROMACS version: 2023.3
GROMACS modification: No
When solvating my molecule (in this case a drug moluecle, furosemide) the generated solvated coordinate file with acetone as the solvent causes an atom numbering mismatch with the topology file. I’m able to resolve the issue by recording the .gro file by switching the order of the drug molecule and the first solvent molecule (i.e. copying and pasting the sovlent molecule first in the order of the .gro file instead of it being the drug molecule). I’m unsure why this happens and if there is something wrong with my set up.
Here’s the relevant portions of my .gro files:
WITHOUT SOLVENT
Great Red Owns Many ACres of Sand
32
1fse CL1 1 -0.109 0.294 -0.065
1fse S2 2 -0.373 0.120 0.001
1fse O3 3 0.474 0.037 -0.043
1fse O4 4 -0.373 0.244 -0.076
1fse O5 5 -0.473 0.018 -0.026
1fse O6 6 -0.167 -0.342 0.105
1fse O7 7 0.011 -0.371 -0.033
1fse N8 8 0.162 -0.138 -0.040
1fse N9 9 -0.378 0.158 0.168
1fse C10 10 0.035 -0.077 -0.030
1fse C11 11 -0.214 0.048 -0.012
1fse C12 12 -0.079 -0.152 -0.001
1fse C13 13 -0.204 -0.090 0.008
1fse C14 14 0.272 -0.077 -0.107
1fse C15 15 0.024 0.061 -0.049
1fse C16 16 -0.101 0.123 -0.040
1fse C17 17 0.342 0.024 -0.021
WITH SOLVENT
Giant Rising Ordinary Mutants for A Clerical Setup
7322
2ACE O1 33 0.000 0.186 0.000
2ACE C1 34 0.000 0.064 0.000
2ACE C2 35 0.000 -0.015 0.129
2ACE C3 36 0.000 -0.015 -0.129
2ACE H1 37 0.000 0.052 0.214
2ACE H2 38 -0.088 -0.080 0.133
2ACE H3 39 0.088 -0.080 0.133
2ACE H4 40 0.000 0.052 -0.214
2ACE H5 41 0.088 -0.080 -0.133
2ACE H6 42 -0.088 -0.080 -0.133
1fse CL1 1 4.417 4.846 4.472
1fse S2 2 4.153 4.672 4.538
1fse O3 3 5.000 4.589 4.494
1fse O4 4 4.153 4.796 4.461
1fse O5 5 4.053 4.570 4.511
1fse O6 6 4.359 4.210 4.642
1fse O7 7 4.537 4.181 4.504
Any help would be greatly appreciated!