Hello all,
I am stuck with a rather puzzling problem. I am trying to use tiMerge in
parmed to create a merge topology for a pair of ligands.
The non-softcore atoms share exactly the same coordinates and I can see
that their orders match using both printDetails and inspection of the PDB
that is loaded into parmed match (see data below). However, parmed gives
back an error saying that the nonsoftcore atoms in mol1mask and mol2mask
must be the same. This occurs even with very high tolerance settings.
Can anyone help me figure out what is going on?
I am running on AMBER18.
-Dr. Wesley Botello-Smith
------PARMED OUTPUT------
> parm doku_yoda_only.dual.parm7
Adding prmtop doku_yoda_only.dual.parm7 to parm list.
doku_yoda_only.dual.parm7 is the active parm.
> loadCoordinates doku_yoda_only.dual.pdb
Adding coordinates to doku_yoda_only.dual.parm7 from doku_yoda_only.dual.pdb
> tiMerge :1 :2 :1.C8,N2,N1,C9,S2,C10,C11,H6,N3,C12,H7,C13,H8,N4 :2.C8,N2,N1,C9,O,C10,C11,H6,C12,H7,C13,H8,N3,H9
tol 10000000000
Merging molecules [:1] [:2] with sc mask
[:1.C8,N2,N1,C9,S2,C10,C11,H6,N3,C12,H7,C13,H8,N4]
[:2.C8,N2,N1,C9,O,C10,C11,H6,C12,H7,C13,H8,N3,H9]
Action tiMerge failed
TiMergeError: The number of nonsoftcore atoms in mol1mask and
mol2mask must be the same. Check the masks. If these look correct try using
a larger tolerance.
> printDetails :1&!(.C8,N2,N1,C9,S2,C10,C11,H6,N3,C12,H7,C13,H8,N4)
The mask :1&!(.C8,N2,N1,C9,S2,C10,C11,H6,N3,C12,H7,C13,H8,N4) matches 15
atoms:
ATOM RES RESNAME NAME TYPE At.# LJ Radius LJ Depth
Mass Charge GB Radius GB Screen
5 1 YOD S1 SG31 16 2.0000 0.4500
32.0600 -0.0900 1.8000 0.9600
6 1 YOD C7 CG32 6 2.0100 0.0560
12.0110 0.3340 1.7000 0.7200
7 1 YOD C6 CG2R 6 1.9924 0.0700
12.0110 -0.2440 1.7000 0.7200
8 1 YOD C1 CG2R 6 1.9924 0.0700
12.0110 -0.0200 1.7000 0.7200
9 1 YOD CL1 CLGR 17 1.8600 0.2300
35.4530 -0.1460 1.5000 0.8000
10 1 YOD C2 CG2R 6 1.9924 0.0700
12.0110 -0.1070 1.7000 0.7200
11 1 YOD C3 CG2R 6 1.9924 0.0700
12.0110 -0.1170 1.7000 0.7200
12 1 YOD C4 CG2R 6 1.9924 0.0700
12.0110 -0.1070 1.7000 0.7200
13 1 YOD C5 CG2R 6 1.9924 0.0700
12.0110 -0.0200 1.7000 0.7200
14 1 YOD CL2 CLGR 17 1.8600 0.2300
35.4530 -0.1460 1.5000 0.8000
15 1 YOD H4 HGA2 1 1.3400 0.0350
1.0080 0.0900 1.3000 0.8500
16 1 YOD H5 HGA2 1 1.3400 0.0350
1.0080 0.0900 1.3000 0.8500
17 1 YOD H1 HGR6 1 1.1000 0.0460
1.0080 0.1650 1.3000 0.8500
18 1 YOD H2 HGR6 1 1.3582 0.0300
1.0080 0.1150 1.3000 0.8500
19 1 YOD H3 HGR6 1 1.1000 0.0460
1.0080 0.1650 1.3000 0.8500
> printDetails :2&!(.C8,N2,N1,C9,O,C10,C11,H6,C12,H7,C13,H8,N3,H9)
The mask :2&!(.C8,N2,N1,C9,O,C10,C11,H6,C12,H7,C13,H8,N3,H9) matches 15
atoms:
ATOM RES RESNAME NAME TYPE At.# LJ Radius LJ Depth
Mass Charge GB Radius GB Screen
34 2 DOK S1 SG31 16 2.0000 0.4500
32.0600 -0.0650 1.8000 0.9600
35 2 DOK C7 CG32 6 2.0100 0.0560
12.0110 0.3190 1.7000 0.7200
36 2 DOK C6 CG2R 6 1.9924 0.0700
12.0110 -0.2580 1.7000 0.7200
37 2 DOK C1 CG2R 6 1.9924 0.0700
12.0110 -0.0380 1.7000 0.7200
38 2 DOK CL1 CLGR 17 1.8600 0.2300
35.4530 -0.1670 1.5000 0.8000
39 2 DOK C2 CG2R 6 1.9924 0.0700
12.0110 -0.0870 1.7000 0.7200
40 2 DOK C3 CG2R 6 1.9924 0.0700
12.0110 -0.1230 1.7000 0.7200
41 2 DOK C4 CG2R 6 1.9924 0.0700
12.0110 -0.0870 1.7000 0.7200
42 2 DOK C5 CG2R 6 1.9924 0.0700
12.0110 -0.0380 1.7000 0.7200
43 2 DOK CL2 CLGR 17 1.8600 0.2300
35.4530 -0.1670 1.5000 0.8000
44 2 DOK H4 HGA2 1 1.3400 0.0350
1.0080 0.0900 1.3000 0.8500
45 2 DOK H5 HGA2 1 1.3400 0.0350
1.0080 0.0900 1.3000 0.8500
46 2 DOK H1 HGR6 1 1.1000 0.0460
1.0080 0.1440 1.3000 0.8500
47 2 DOK H2 HGR6 1 1.3582 0.0300
1.0080 0.1150 1.3000 0.8500
48 2 DOK H3 HGR6 1 1.1000 0.0460
1.0080 0.1440 1.3000 0.8500
------ ------ ------
------ PDB File ------
ATOM 5 S1 YOD 1 21.230 20.060 19.980 1.00 0.00
S
ATOM 6 C7 YOD 1 21.060 21.850 19.980 1.00 0.00
C
ATOM 7 C6 YOD 1 22.430 22.550 19.980 1.00 0.00
C
ATOM 8 C1 YOD 1 23.760 21.970 19.980 1.00 0.00
C
ATOM 9 CL1 YOD 1 24.190 20.280 19.980 1.00 0.00
CL
ATOM 10 C2 YOD 1 24.900 22.770 19.980 1.00 0.00
C
ATOM 11 C3 YOD 1 24.810 24.150 19.980 1.00 0.00
C
ATOM 12 C4 YOD 1 23.550 24.750 19.980 1.00 0.00
C
ATOM 13 C5 YOD 1 22.390 23.970 19.980 1.00 0.00
C
ATOM 14 CL2 YOD 1 20.870 24.830 19.980 1.00 0.00
CL
ATOM 15 H4 YOD 1 20.500 22.210 20.880 1.00 0.00
H
ATOM 16 H5 YOD 1 20.500 22.210 19.080 1.00 0.00
H
ATOM 17 H1 YOD 1 25.860 22.280 19.980 1.00 0.00
H
ATOM 18 H2 YOD 1 25.710 24.750 19.980 1.00 0.00
H
ATOM 19 H3 YOD 1 23.480 25.830 19.980 1.00 0.00
H
...
ATOM 34 S1 DOK 2 21.230 20.060 19.980 1.00 0.00
S
ATOM 35 C7 DOK 2 21.060 21.850 19.980 1.00 0.00
C
ATOM 36 C6 DOK 2 22.430 22.550 19.980 1.00 0.00
C
ATOM 37 C1 DOK 2 23.760 21.970 19.980 1.00 0.00
C
ATOM 38 CL1 DOK 2 24.200 20.270 19.980 1.00 0.00
CL
ATOM 39 C2 DOK 2 24.900 22.770 19.980 1.00 0.00
C
ATOM 40 C3 DOK 2 24.810 24.150 19.980 1.00 0.00
C
ATOM 41 C4 DOK 2 23.550 24.750 19.980 1.00 0.00
C
ATOM 42 C5 DOK 2 22.390 23.970 19.980 1.00 0.00
C
ATOM 43 CL2 DOK 2 20.860 24.830 19.980 1.00 0.00
CL
ATOM 44 H4 DOK 2 20.500 22.210 20.880 1.00 0.00
H
ATOM 45 H5 DOK 2 20.500 22.210 19.080 1.00 0.00
H
ATOM 46 H1 DOK 2 25.860 22.280 19.980 1.00 0.00
H
ATOM 47 H2 DOK 2 25.710 24.750 19.980 1.00 0.00
H
ATOM 48 H3 DOK 2 23.480 25.830 19.980 1.00 0.00
H
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Received on Fri Dec 21 2018 - 09:30:03 PST
