Wrong boundary atoms provided with "-find_bound True"
In attachment the KATG.top topology file, the prod.gro coordinate file, the VMD visualisation file prod.vmd to see the QM part:
set sel [ atomselect top "((resname HEM MEX TRX TYX and residue < 717) or (resid 246 356 75 79 108 and residue < 715) or (resid 106 120 297 and (sidechain or name CA) and residue < 715) or (resid 61 62 169 and (sidechain or name CA) and residue < 715) or (resname INH and resid 719) or (same residue as (water within 6 of (resname HEM MEX TRX TYX and residue < 717))) or (same residue as (water within 6 of (resid 106 120 297 and (sidechain or name CA) and residue < 715))) or (same residue as (water within 6 of (resid 61 62 169 and (sidechain or name CA) and residue < 715))) or (same residue as (water within 6 of (resname INH and resid 719)))) and not (protein and (name O N C H HA CA))" ]
and the corresponding 14 boundary atoms (green points in the VMD visualisation state):
set sel_link [ atomselect top "((resname HEM MEX TRX TYX and residue < 717) or (resid 246 356 75 79 108 and residue < 715) or (resid 106 120 297 and (sidechain or name CA) and residue < 715) or (resid 61 62 169 and (sidechain or name CA) and residue < 715) or (resname INH and resid 719) or (same residue as (water within 6 of (resname HEM MEX TRX TYX and residue < 717))) or (same residue as (water within 6 of (resid 106 120 297 and (sidechain or name CA) and residue < 715))) or (same residue as (water within 6 of (resid 61 62 169 and (sidechain or name CA) and residue < 715))) or (same residue as (water within 6 of (resname INH and resid 719)))) and name CA" ]
If I ask mimicpy though the VMD plugin to give me the list of boundary atoms with the command:
prepqm -top KATG.top -coords prod.gro -sele $sel -pad 0.35 -out ZZZ.inp -find_bound True
I get the message:
"Boundary atoms were automatically set. The following atom(s) were marked as boundary atoms:
+---------------------+
| Atom | Residue |
+---------------------+
| 21895 O | 1447 WAT |
+---------------------+
| 21896 H1 | 1447 WAT |
+---------------------+
| 1161 CB | 75 ARG |
+---------------------+
| 21897 H2 | 1447 WAT |
+---------------------+
| 21910 O | 1452 WAT |
+---------------------+
| 3737 CB | 246 HID |
+---------------------+
| 939 CB | 61 TRP |
+---------------------+
| 2608 CB | 169 TRP |
+---------------------+
| 1842 CB | 120 TRP |
+---------------------+
| 1212 CB | 78 TRX |
+---------------------+
| 963 CB | 62 TRP |
+---------------------+
| 1605 CB | 106 TRP |
+---------------------+
| 4429 CB | 297 TRP |
+---------------------+
| 3535 CB | 231 MEX |
+---------------------+
| 1235 CB | 79 HID |
+---------------------+
| 3159 CB | 205 TYX |
+---------------------+
| 21851 N2 | 1435 INH |
+---------------------+
| 21852 H1 | 1435 INH |
+---------------------+
| 21853 H2 | 1435 INH |
+---------------------+
| 1643 CB | 108 ASP |
+---------------------+
| 5356 CB | 356 ASP |
+---------------------+
"
which of course is wrong both in the number of atoms and in which atoms are selected.