GROMACS version: 2020.6
GROMACS modification: No
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Hi Gromacs team,
I am adding a new cap residue to the charmm36 forcefield. However, there is an H atom in the FOR residue (aldehyde group).
ATOM 1608 C FOR B 111 -4.401 14.796 -50.833 1.00 0.00
ATOM 1609 O FOR B 111 -4.530 15.342 -51.930 1.00 0.00
ATOM 1610 H FOR B 111 -3.410 14.517 -50.476 1.00 0.00
ATOM 1611 N MET B 112 -5.460 14.552 -50.092 1.00 0.00
ATOM 1612 CA MET B 112 -6.810 14.903 -50.519 1.00 0.00
ATOM 1613 C MET B 112 -7.861 14.498 -49.479 1.00 0.00
ATOM 1614 O MET B 112 -8.159 15.263 -48.560 1.00 0.00
ATOM 1615 H MET B 112 -5.326 14.099 -49.187 1.00 0.00
…
As pdb2gmx processes the PDB file, it will map the original atom name (H) to its alias (HN) according to the .arn file.
The arn file is as follow:
; atom renaming specification
; residue gromacs forcefield
* H HN
In this sentence is * representing all residues? I am curious if there are any other more complex selection syntaxes to achieve more fine selection. eg. in this situation, I would like to use the syntax like:
"Select all and not FOR residue"
Best wishes,
Yang