how to reset resid for protein and water and ions

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Jingjing Ji

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Aug 4, 2022, 12:57:30 PMAug 4
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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
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