Dear Amber Community,
I’m trying to parameterize a Ru-bipyridine dye with MCPB. Step 1 is rejected my PDB when the atom name for H, C, or N is more than one character. For example,
A PDB that works:
ATOM 1 RU RU A 1 19.636 4.619 10.390 0.40 17.85 RU
ATOM 2 C MBP A 2 14.496 1.208 10.292 0.40 22.65 C
ATOM 3 C MBP A 2 15.752 2.042 10.319 0.40 21.47 C
ATOM 4 C MBP A 2 15.726 3.363 9.893 0.40 23.24 C
ATOM 5 C MBP A 2 16.907 4.092 9.934 0.40 19.31 C
ATOM 6 C MBP A 2 16.950 1.492 10.767 0.40 20.67 C
ATOM 7 C MBP A 2 18.135 2.241 10.805 0.40 19.72 C
ATOM 8 N MBP A 2 18.118 3.531 10.396 0.40 24.51 N
ATOM 9 N MBP A 2 18.419 5.901 9.704 0.40 19.77 N
ATOM 10 C MBP A 2 18.732 7.174 9.383 0.40 20.78 C
ATOM 11 C MBP A 2 17.743 8.057 8.893 0.40 17.23 C
ATOM 12 C MBP A 2 17.070 5.503 9.526 0.40 18.52 C
ATOM 13 C MBP A 2 16.111 6.320 9.045 0.40 18.27 C
ATOM 14 C MBP A 2 16.426 7.635 8.706 0.40 20.25 C
ATOM 15 C MBP A 2 15.365 8.570 8.162 0.40 18.23 C
ATOM 16 H MBP A 2 19.049 1.788 11.158 0.40 0.00 H
ATOM 17 H MBP A 2 14.803 3.799 9.541 0.40 0.00 H
ATOM 18 H MBP A 2 15.102 5.955 8.923 0.40 0.00 H
ATOM 19 H MBP A 2 18.022 9.075 8.662 0.40 0.00 H
ATOM 20 H MBP A 2 19.746 7.527 9.500 0.40 0.00 H
ATOM 21 H MBP A 2 14.716 0.207 10.662 0.40 0.00 H
ATOM 22 H MBP A 2 13.739 1.670 10.925 0.40 0.00 H
ATOM 23 H MBP A 2 14.124 1.144 9.270 0.40 0.00 H
ATOM 24 H MBP A 2 16.982 0.464 11.097 0.40 0.00 H
ATOM 25 H MBP A 2 14.414 8.042 8.096 0.40 0.00 H
ATOM 26 H MBP A 2 15.259 9.427 8.828 0.40 0.00 H
ATOM 27 H MBP A 2 15.658 8.915 7.171 0.40 0.00 H
ATOM 28 N UBP A 3 20.083 4.412 8.587 0.40 19.97 N
ATOM 29 C UBP A 3 19.379 3.659 7.711 0.40 20.78 C
ATOM 30 C UBP A 3 19.813 3.586 6.384 0.40 23.53 C
ATOM 31 C UBP A 3 20.953 4.252 5.939 0.40 21.35 C
ATOM 32 C UBP A 3 21.231 5.098 8.147 0.40 17.35 C
ATOM 33 C UBP A 3 21.681 5.024 6.833 0.40 20.73 C
ATOM 34 C UBP A 3 21.878 5.854 9.235 0.40 20.42 C
ATOM 35 C UBP A 3 23.037 6.623 9.115 0.40 22.55 C
ATOM 36 C UBP A 3 23.509 7.279 10.235 0.40 17.44 C
ATOM 37 C UBP A 3 22.830 7.134 11.438 0.40 19.30 C
ATOM 38 C UBP A 3 21.672 6.357 11.534 0.40 16.66 C
ATOM 39 N UBP A 3 21.180 5.710 10.454 0.40 20.20 N
ATOM 40 H UBP A 3 21.169 6.277 12.487 0.40 0.00 H
ATOM 41 H UBP A 3 24.393 7.898 10.185 0.40 0.00 H
ATOM 42 H UBP A 3 23.195 7.628 12.327 0.40 0.00 H
ATOM 43 H UBP A 3 23.542 6.694 8.163 0.40 0.00 H
ATOM 44 H UBP A 3 22.572 5.558 6.536 0.40 0.00 H
ATOM 45 H UBP A 3 19.233 2.989 5.696 0.40 0.00 H
ATOM 46 H UBP A 3 21.262 4.164 4.908 0.40 0.00 H
ATOM 47 H UBP A 3 18.499 3.128 8.041 0.40 0.00 H
ATOM 48 N UBP A 4 20.863 3.346 11.041 0.40 21.73 N
ATOM 49 C UBP A 4 21.582 2.547 10.228 0.40 16.57 C
ATOM 50 C UBP A 4 22.473 1.621 10.791 0.40 19.58 C
ATOM 51 C UBP A 4 22.630 1.514 12.177 0.40 20.59 C
ATOM 52 C UBP A 4 21.014 3.241 12.444 0.40 18.23 C
ATOM 53 C UBP A 4 21.894 2.333 13.029 0.40 21.19 C
ATOM 54 C UBP A 4 20.125 4.194 13.139 0.40 20.44 C
ATOM 55 C UBP A 4 20.018 4.380 14.517 0.40 20.79 C
ATOM 56 C UBP A 4 19.137 5.337 14.997 0.40 20.98 C
ATOM 57 C UBP A 4 18.400 6.086 14.083 0.40 21.18 C
ATOM 58 C UBP A 4 18.524 5.882 12.706 0.40 19.55 C
ATOM 59 N UBP A 4 19.379 4.958 12.213 0.40 21.67 N
ATOM 60 H UBP A 4 21.469 2.624 9.157 0.40 0.00 H
ATOM 61 H UBP A 4 23.054 0.973 10.151 0.40 0.00 H
ATOM 62 H UBP A 4 23.323 0.795 12.588 0.40 0.00 H
ATOM 63 H UBP A 4 22.018 2.249 14.099 0.40 0.00 H
ATOM 64 H UBP A 4 20.616 3.784 15.190 0.40 0.00 H
ATOM 65 H UBP A 4 19.033 5.490 16.061 0.40 0.00 H
ATOM 66 H UBP A 4 17.715 6.844 14.434 0.40 0.00 H
ATOM 67 H UBP A 4 17.932 6.467 12.018 0.40 0.00 H
Versus a PDB that is rejected
ATOM 1 RU RU A 1 19.636 4.619 10.390 0.40 17.85 RU
ATOM 2 C38 MBP A 2 14.496 1.208 10.292 0.40 22.65 C
ATOM 3 C17 MBP A 2 15.752 2.042 10.319 0.40 21.47 C
ATOM 4 C18 MBP A 2 15.726 3.363 9.893 0.40 23.24 C
ATOM 5 C19 MBP A 2 16.907 4.092 9.934 0.40 19.31 C
ATOM 6 C16 MBP A 2 16.950 1.492 10.767 0.40 20.67 C
ATOM 7 C15 MBP A 2 18.135 2.241 10.805 0.40 19.72 C
ATOM 8 N14 MBP A 2 18.118 3.531 10.396 0.40 24.51 N
ATOM 9 N25 MBP A 2 18.419 5.901 9.704 0.40 19.77 N
ATOM 10 C24 MBP A 2 18.732 7.174 9.383 0.40 20.78 C
ATOM 11 C23 MBP A 2 17.743 8.057 8.893 0.40 17.23 C
ATOM 12 C20 MBP A 2 17.070 5.503 9.526 0.40 18.52 C
ATOM 13 C21 MBP A 2 16.111 6.320 9.045 0.40 18.27 C
ATOM 14 C22 MBP A 2 16.426 7.635 8.706 0.40 20.25 C
ATOM 15 C39 MBP A 2 15.365 8.570 8.162 0.40 18.23 C
ATOM 16 HC15 MBP A 2 19.049 1.788 11.158 0.40 0.00 H
ATOM 17 HC18 MBP A 2 14.803 3.799 9.541 0.40 0.00 H
ATOM 18 HC21 MBP A 2 15.102 5.955 8.923 0.40 0.00 H
ATOM 19 HC23 MBP A 2 18.022 9.075 8.662 0.40 0.00 H
ATOM 20 HC24 MBP A 2 19.746 7.527 9.500 0.40 0.00 H
ATOM 21 H381 MBP A 2 14.716 0.207 10.662 0.40 0.00 H
ATOM 22 H382 MBP A 2 13.739 1.670 10.925 0.40 0.00 H
ATOM 23 H383 MBP A 2 14.124 1.144 9.270 0.40 0.00 H
ATOM 24 HC16 MBP A 2 16.982 0.464 11.097 0.40 0.00 H
ATOM 25 H391 MBP A 2 14.414 8.042 8.096 0.40 0.00 H
ATOM 26 H392 MBP A 2 15.259 9.427 8.828 0.40 0.00 H
ATOM 27 H393 MBP A 2 15.658 8.915 7.171 0.40 0.00 H
ATOM 28 N2 UBP A 3 20.083 4.412 8.587 0.40 19.97 N
ATOM 29 C3 UBP A 3 19.379 3.659 7.711 0.40 20.78 C
ATOM 30 C4 UBP A 3 19.813 3.586 6.384 0.40 23.53 C
ATOM 31 C5 UBP A 3 20.953 4.252 5.939 0.40 21.35 C
ATOM 32 C7 UBP A 3 21.231 5.098 8.147 0.40 17.35 C
ATOM 33 C6 UBP A 3 21.681 5.024 6.833 0.40 20.73 C
ATOM 34 C8 UBP A 3 21.878 5.854 9.235 0.40 20.42 C
ATOM 35 C9 UBP A 3 23.037 6.623 9.115 0.40 22.55 C
ATOM 36 C10 UBP A 3 23.509 7.279 10.235 0.40 17.44 C
ATOM 37 C11 UBP A 3 22.830 7.134 11.438 0.40 19.30 C
ATOM 38 C12 UBP A 3 21.672 6.357 11.534 0.40 16.66 C
ATOM 39 N13 UBP A 3 21.180 5.710 10.454 0.40 20.20 N
ATOM 40 HC12 UBP A 3 21.169 6.277 12.487 0.40 0.00 H
ATOM 41 HC10 UBP A 3 24.393 7.898 10.185 0.40 0.00 H
ATOM 42 HC11 UBP A 3 23.195 7.628 12.327 0.40 0.00 H
ATOM 43 HC9 UBP A 3 23.542 6.694 8.163 0.40 0.00 H
ATOM 44 HC6 UBP A 3 22.572 5.558 6.536 0.40 0.00 H
ATOM 45 HC4 UBP A 3 19.233 2.989 5.696 0.40 0.00 H
ATOM 46 HC5 UBP A 3 21.262 4.164 4.908 0.40 0.00 H
ATOM 47 HC3 UBP A 3 18.499 3.128 8.041 0.40 0.00 H
ATOM 48 N26 UBP A 4 20.863 3.346 11.041 0.40 21.73 N
ATOM 49 C27 UBP A 4 21.582 2.547 10.228 0.40 16.57 C
ATOM 50 C28 UBP A 4 22.473 1.621 10.791 0.40 19.58 C
ATOM 51 C29 UBP A 4 22.630 1.514 12.177 0.40 20.59 C
ATOM 52 C31 UBP A 4 21.014 3.241 12.444 0.40 18.23 C
ATOM 53 C30 UBP A 4 21.894 2.333 13.029 0.40 21.19 C
ATOM 54 C32 UBP A 4 20.125 4.194 13.139 0.40 20.44 C
ATOM 55 C33 UBP A 4 20.018 4.380 14.517 0.40 20.79 C
ATOM 56 C34 UBP A 4 19.137 5.337 14.997 0.40 20.98 C
ATOM 57 C35 UBP A 4 18.400 6.086 14.083 0.40 21.18 C
ATOM 58 C36 UBP A 4 18.524 5.882 12.706 0.40 19.55 C
ATOM 59 N37 UBP A 4 19.379 4.958 12.213 0.40 21.67 N
ATOM 60 HC27 UBP A 4 21.469 2.624 9.157 0.40 0.00 H
ATOM 61 HC28 UBP A 4 23.054 0.973 10.151 0.40 0.00 H
ATOM 62 HC29 UBP A 4 23.323 0.795 12.588 0.40 0.00 H
ATOM 63 HC30 UBP A 4 22.018 2.249 14.099 0.40 0.00 H
ATOM 64 HC33 UBP A 4 20.616 3.784 15.190 0.40 0.00 H
ATOM 65 HC34 UBP A 4 19.033 5.490 16.061 0.40 0.00 H
ATOM 66 HC35 UBP A 4 17.715 6.844 14.434 0.40 0.00 H
ATOM 67 HC36 UBP A 4 17.932 6.467 12.018 0.40 0.00 H
With the error message:
***Creating the small model...
It contains the residue 1-RU as normal.
It contains the residue 2-MBP as normal.
It contains the residue 3-UBP as normal.
It contains the residue 4-UBP as normal.
Totally there are 67 atoms in the small model.
Totally there are 303 electrons in the small model.
***Creating the standard model...
It contains the residue 1-RU as normal.
It contains the residue 2-MBP as normal.
Traceback (most recent call last):
File "/opt/anaconda3/envs/AmberTools20/bin/MCPB.py", line 643, in <module>
gene_model_files(orpdbf, ionids, addres, addbpairs, gname, ff_choice,
File "/opt/anaconda3/envs/AmberTools20/lib/python3.9/site-packages/pymsmt/mcpb/gene_model_files.py", line 1906, in gene_model_files
build_standard_model(mol, reslist, cutoff, msresids, outf, ionids,
File "/opt/anaconda3/envs/AmberTools20/lib/python3.9/site-packages/pymsmt/mcpb/gene_model_files.py", line 1471, in build_standard_model
attype = libdict[resname + '-' + atname][0]
KeyError: 'MBP-C38'
What am I missing with the formatting? I’ve tried generating PDBs with VMD and GaussView, but the result is the same.
Best,
Matthew
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Received on Tue Jan 11 2022 - 09:00:02 PST
