Hello,
I tried to insert several hydrated NA (NA+SOL) into the "protein+water (SOL)" system using gmx command (gmx insert-molecules). After that, I found the resulting .gro file is:
1641SOL H2 8335 8.395 1.809 2.386
1642SOL OH2 8336 8.062 1.761 1.989
1642SOL H1 8337 7.976 1.753 2.032
1642SOL H2 8338 8.069 1.855 1.968
1643NA NA 8339 -3.013 8.185 -4.297
1644SOL OH2 8340 -3.267 8.101 -4.267
1644SOL H1 8341 -3.313 8.038 -4.320
1644SOL H2 8342 -3.326 8.119 -4.194
1645SOL OH2 8343 -2.677 8.316 -4.230
1645SOL H1 8344 -2.729 8.295 -4.308
1645SOL H2 8345 -2.664 8.232 -4.188
1646SOL OH2 8346 -2.935 7.983 -4.368
1646SOL H1 8347 -2.954 7.889 -4.371
1646SOL H2 8348 -2.850 7.992 -4.410
1647SOL OH2 8349 -2.854 8.276 -4.449
1647SOL H1 8350 -2.854 8.218 -4.526
1647SOL H2 8351 -2.838 8.363 -4.486
1648SOL OH2 8352 -3.232 8.438 -4.428
1648SOL H1 8353 -3.204 8.379 -4.497
1648SOL H2 8354 -3.171 8.422 -4.356
1649SOL OH2 8355 -3.068 8.401 -4.186
1649SOL H1 8356 -3.018 8.404 -4.105
1649SOL H2 8357 -3.152 8.443 -4.165
1650SOL OH2 8358 -2.918 8.160 -4.095
1650SOL H1 8359 -2.969 8.102 -4.040
1650SOL H2 8360 -2.908 8.240 -4.044
1651SOL OH2 8361 -3.114 8.179 -4.518
1651SOL H1 8362 -3.048 8.129 -4.565
1651SOL H2 8363 -3.176 8.114 -4.486
1652NA NA 8364 4.306 2.238 -7.256
1653SOL OH2 8365 4.199 2.387 -7.060
For this .gro file, I like to write protein first, and then water(SOL), and finally are NA. Also, I like to reset resid for them. Can any commands in MDAnalysis help realize this process?
Thank you!
Jingjing