AMBER Archive (2006)

Subject: AMBER: RMSD calculation between ligands

From: Stefan Henrich (stefan.henrich_at_eml-r.villa-bosch.de)
Date: Fri May 12 2006 - 07:09:15 CDT

Hi,

is there any possibility to calculate RMSD between a ligand of a
pdb-file (eg. retrieved xray structure from PDB) and the same ligand in
sdf-format (or mol2) from docking?

Both structures are chemically identical and already protonated. The
problem is that they have different atom names and the atoms are in a
different order, because the first one is taken from xray structure and
the second one was sketched as an SD file, 3D coordinates were generated
by CORINA and then it was re-docked by GOLD into the receptor of the
xray structure.

For both complexes (receptor with xray/docking solution) I calculate the
ligand parameters with ANTECHAMBER, read them into tleap (AMBER8) and do
minimization in sander, so I have parm/prep files, coordinates, topology
and minimized pdb files. Because of missing bond types in the ligand
pdb-file of the xray structure, I modified the calculation of the
parm/prep files by using the bond information of the SDF as an
additional file:
antechamber -i xray.pdb -fi pdb -a ligand.sdf -fa mdl -ao bond -j 5 -o
PREP_AC.AC -fo ac -c bcc -rn LIG -nc 1 -pf y
atomtype -i PREP_AC.AC -o PREP_TYPE.AC -d my_ATOMTYPE_GFF.DEF
prepgen -i PREP_TYPE.AC -o xray.prep -f int -rn LIG
parmchk -i xray.prep -f prepi -o xray.parm -p gaff.dat

I tried to run ptraj with the coordination files of the two complexes
together with one of the topology file. The number of atoms were the
same, so I got no error message, but because of the different order of
the atoms of the ligand, I couldn't get any reliable RMSD.

Do you have any idea to handle this problem? Thank you very much for any
advice.

Stefan

C21H26FN4O2
  -GOLD- 32906 0103D 1 1.00000 0.00000
CORINA 3.20 0003 11.05.2005
 52 55 0 0 0 0 0 0 0 0 2 V2000
    8.5706 1.6589 23.6546 C 0 0 0 0 0 0 0 0 0 0 0 0
    7.9496 0.7067 22.9246 F 0 0 0 0 0 0 0 0 0 0 0 0
    8.8638 2.8782 23.0844 C 0 0 0 0 0 0 0 0 0 0 0 0
    9.5024 3.8599 23.8322 C 0 0 0 0 0 0 0 0 0 0 0 0
    9.8520 3.6128 25.1735 C 0 0 0 0 0 0 0 0 0 0 0 0
    9.5539 2.3773 25.7479 C 0 0 0 0 0 0 0 0 0 0 0 0
   10.4537 4.7348 25.6437 N 0 0 0 0 0 0 0 0 0 0 0 0
   10.4964 5.6395 24.6968 C 0 0 0 0 0 0 0 0 0 0 0 0
   11.0789 6.9901 24.8379 C 0 0 0 0 0 0 0 0 0 0 0 0
   11.8588 7.5297 23.8101 C 0 0 0 0 0 0 0 0 0 0 0 0
   12.4023 8.8018 23.9532 C 0 0 0 0 0 0 0 0 0 0 0 0
   13.1613 9.3330 22.9575 O 0 0 0 0 0 0 0 0 0 0 0 0
   12.1701 9.5280 25.1098 C 0 0 0 0 0 0 0 0 0 0 0 0
   11.3984 8.9931 26.1273 C 0 0 0 0 0 0 0 0 0 0 0 0
   12.0847 6.8144 22.6773 O 0 0 0 0 0 0 0 0 0 0 0 0
   10.8484 7.7359 25.9962 C 0 0 0 0 0 0 0 0 0 0 0 0
    9.9200 5.1452 23.5564 N 0 0 0 0 0 0 0 0 0 0 0 0
    8.9092 1.4038 24.9920 C 0 0 0 0 0 0 0 0 0 0 0 0
    8.5857 0.0958 25.5972 C 0 0 0 0 0 0 0 0 0 0 0 0
    8.0927 0.0376 26.8339 N 0 3 0 0 0 0 0 0 0 0 0 0
    8.7868 -1.0258 24.9066 N 0 0 0 0 0 0 0 0 0 0 0 0
    8.5974 3.0710 22.0558 H 0 0 0 0 0 0 0 0 0 0 0 0
    9.8187 2.1790 26.7760 H 0 0 0 0 0 0 0 0 0 0 0 0
   12.5934 10.5156 25.2185 H 0 0 0 0 0 0 0 0 0 0 0 0
   11.2224 9.5656 27.0260 H 0 0 0 0 0 0 0 0 0 0 0 0
   12.4131 5.9190 22.8364 H 0 0 0 0 0 0 0 0 0 0 0 0
   10.2432 7.3256 26.7910 H 0 0 0 0 0 0 0 0 0 0 0 0
    9.8234 5.6126 22.7118 H 0 0 0 0 0 0 0 0 0 0 0 0
    7.9463 0.8542 27.3367 H 0 0 0 0 0 0 0 0 0 0 0 0
    7.8801 -0.8213 27.2313 H 0 0 0 0 0 0 0 0 0 0 0 0
    9.1457 -0.9835 24.0065 H 0 0 0 0 0 0 0 0 0 0 0 0
    8.5744 -1.8849 25.3041 H 0 0 0 0 0 0 0 0 0 0 0 0
   14.2281 8.5263 22.4540 C 0 0 0 0 0 0 0 0 0 0 0 0
   13.9968 8.2443 20.9681 C 0 0 0 0 0 0 0 0 0 0 0 0
   15.5551 9.2667 22.6320 C 0 0 0 0 0 0 0 0 0 0 0 0
   15.5087 10.5886 21.8632 C 0 0 0 0 0 0 0 0 0 0 0 0
   15.2775 10.3066 20.3774 C 0 0 0 0 0 0 0 0 0 0 0 0
   13.9504 9.5662 20.1993 C 0 0 0 0 0 0 0 0 0 0 0 0
   15.7863 9.5488 24.1179 C 0 0 0 0 0 0 0 0 0 0 0 0
   14.2611 7.5846 23.0019 H 0 0 0 0 0 0 0 0 0 0 0 0
   14.8104 7.6290 20.5842 H 0 0 0 0 0 0 0 0 0 0 0 0
   13.0513 7.7168 20.8413 H 0 0 0 0 0 0 0 0 0 0 0 0
   16.3688 8.6514 22.2481 H 0 0 0 0 0 0 0 0 0 0 0 0
   14.6951 11.2039 22.2472 H 0 0 0 0 0 0 0 0 0 0 0 0
   16.4542 11.1161 21.9900 H 0 0 0 0 0 0 0 0 0 0 0 0
   15.2445 11.2483 19.8295 H 0 0 0 0 0 0 0 0 0 0 0 0
   16.0912 9.6913 19.9933 H 0 0 0 0 0 0 0 0 0 0 0 0
   13.7857 9.3652 19.1407 H 0 0 0 0 0 0 0 0 0 0 0 0
   13.1367 10.1815 20.5832 H 0 0 0 0 0 0 0 0 0 0 0 0
   16.7332 10.0738 24.2450 H 0 0 0 0 0 0 0 0 0 0 0 0
   14.9742 10.1666 24.5012 H 0 0 0 0 0 0 0 0 0 0 0 0
   15.8165 8.6072 24.6662 H 0 0 0 0 0 0 0 0 0 0 0 0
  1 2 1 0 0 0 0
  1 3 4 0 0 0 0
  1 18 4 0 0 0 0
  3 4 4 0 0 0 0
  3 22 1 0 0 0 0
  4 5 4 0 0 0 0
  4 17 1 0 0 0 0
  5 6 4 0 0 0 0
  5 7 1 0 0 0 0
  6 18 4 0 0 0 0
  6 23 1 0 0 0 0
  7 8 2 0 0 0 0
  8 9 1 0 0 0 0
  8 17 1 0 0 0 0
  9 10 4 0 0 0 0
  9 16 4 0 0 0 0
 10 11 4 0 0 0 0
 10 15 1 0 0 0 0
 11 12 1 0 0 0 0
 11 13 4 0 0 0 0
 13 14 4 0 0 0 0
 13 24 1 0 0 0 0
 14 16 4 0 0 0 0
 14 25 1 0 0 0 0
 15 26 1 0 0 0 0
 16 27 1 0 0 0 0
 17 28 1 0 0 0 0
 18 19 1 0 0 0 0
 19 20 2 0 0 0 0
 19 21 1 0 0 0 0
 20 29 1 0 0 0 0
 20 30 1 0 0 0 0
 21 31 1 0 0 0 0
 21 32 1 0 0 0 0
 33 12 1 0 0 0 0
 33 34 1 0 0 0 0
 33 35 1 0 0 0 0
 35 36 1 0 0 0 0
 36 37 1 0 0 0 0
 34 38 1 0 0 0 0
 37 38 1 0 0 0 0
 35 39 1 0 0 0 0
 33 40 1 0 0 0 0
 34 41 1 0 0 0 0
 34 42 1 0 0 0 0
 35 43 1 0 0 0 0
 36 44 1 0 0 0 0
 36 45 1 0 0 0 0
 37 46 1 0 0 0 0
 37 47 1 0 0 0 0
 38 48 1 0 0 0 0
 38 49 1 0 0 0 0
 39 50 1 0 0 0 0
 39 51 1 0 0 0 0
 39 52 1 0 0 0 0
M CHG 1 20 1
M END

$$$$


C21H26FN4O2
SHcorina_p04180611133D 1 1.00000 0.00000
CORINA 3.20 0003 11.05.2005
 52 55 0 0 0 0 0 0 0 0999 V2000
    0.0210 1.3532 -0.8117 C 0 0 0 0 0 0 0 0 0 0 0 0
    0.0395 0.0034 -0.8663 F 0 0 0 0 0 0 0 0 0 0 0 0
    1.2019 2.0589 -0.8833 C 0 0 0 0 0 0 0 0 0 0 0 0
    1.1868 3.4472 -0.8275 C 0 0 0 0 0 0 0 0 0 0 0 0
   -0.0336 4.1372 -0.6977 C 0 0 0 0 0 0 0 0 0 0 0 0
   -1.2276 3.4199 -0.6254 C 0 0 0 0 0 0 0 0 0 0 0 0
    0.2567 5.4627 -0.6700 N 0 0 0 0 0 0 0 0 0 0 0 0
    1.5522 5.6303 -0.7724 C 0 0 0 0 0 0 0 0 0 0 0 0
    2.2418 6.9371 -0.7791 C 0 0 0 0 0 0 0 0 0 0 0 0
    1.5049 8.1209 -0.6711 C 0 0 0 0 0 0 0 0 0 0 0 0
    2.1639 9.3455 -0.6785 C 0 0 0 0 0 0 0 0 0 0 0 0
    1.4537 10.5006 -0.5733 O 0 0 0 0 0 0 0 0 0 0 0 0
    3.5438 9.3887 -0.7924 C 0 0 0 0 0 0 0 0 0 0 0 0
    4.2729 8.2165 -0.8998 C 0 0 0 0 0 0 0 0 0 0 0 0
    0.1516 8.0747 -0.5599 O 0 0 0 0 0 0 0 0 0 0 0 0
    3.6331 6.9955 -0.8876 C 0 0 0 0 0 0 0 0 0 0 0 0
    2.1713 4.4122 -0.8724 N 0 0 0 0 0 0 0 0 0 0 0 0
   -1.2014 2.0306 -0.6880 C 0 0 0 0 0 0 0 0 0 0 0 0
   -2.4634 1.2663 -0.6180 C 0 0 0 0 0 0 0 0 0 0 0 0
   -2.7859 0.4216 -1.5969 N 0 3 0 0 0 0 0 0 0 0 0 0
   -3.2793 1.4214 0.4240 N 0 0 0 0 0 0 0 0 0 0 0 0
    2.1398 1.5329 -0.9826 H 0 0 0 0 0 0 0 0 0 0 0 0
   -2.1683 3.9409 -0.5254 H 0 0 0 0 0 0 0 0 0 0 0 0
    4.0532 10.3410 -0.7979 H 0 0 0 0 0 0 0 0 0 0 0 0
    5.3484 8.2588 -0.9886 H 0 0 0 0 0 0 0 0 0 0 0 0
   -0.1667 8.0268 0.3519 H 0 0 0 0 0 0 0 0 0 0 0 0
    4.2072 6.0842 -0.9668 H 0 0 0 0 0 0 0 0 0 0 0 0
    3.1250 4.2572 -0.9588 H 0 0 0 0 0 0 0 0 0 0 0 0
   -2.1919 0.3087 -2.3555 H 0 0 0 0 0 0 0 0 0 0 0 0
   -3.6146 -0.0804 -1.5509 H 0 0 0 0 0 0 0 0 0 0 0 0
   -3.0109 1.9781 1.1716 H 0 0 0 0 0 0 0 0 0 0 0 0
   -4.1418 0.9775 0.4350 H 0 0 0 0 0 0 0 0 0 0 0 0
    2.1992 11.7191 -0.5322 C 0 0 1 0 0 0 0 0 0 0 0 0
    2.5333 12.1610 -1.9584 C 0 0 0 0 0 0 0 0 0 0 0 0
    1.3671 12.8031 0.1558 C 0 0 1 0 0 0 0 0 0 0 0 0
    0.0709 13.0244 -0.6264 C 0 0 0 0 0 0 0 0 0 0 0 0
    0.4050 13.4663 -2.0525 C 0 0 0 0 0 0 0 0 0 0 0 0
    1.2371 12.3823 -2.7406 C 0 0 0 0 0 0 0 0 0 0 0 0
    1.0329 12.3612 1.5820 C 0 0 0 0 0 0 0 0 0 0 0 0
    3.1226 11.5614 0.0251 H 0 0 0 0 0 0 0 0 0 0 0 0
    3.1019 13.0903 -1.9270 H 0 0 0 0 0 0 0 0 0 0 0 0
    3.1261 11.3887 -2.4486 H 0 0 0 0 0 0 0 0 0 0 0 0
    1.9357 13.7325 0.1872 H 0 0 0 0 0 0 0 0 0 0 0 0
   -0.4977 12.0950 -0.6577 H 0 0 0 0 0 0 0 0 0 0 0 0
   -0.5219 13.7967 -0.1362 H 0 0 0 0 0 0 0 0 0 0 0 0
   -0.5184 13.6240 -2.6098 H 0 0 0 0 0 0 0 0 0 0 0 0
    0.9736 14.3957 -2.0212 H 0 0 0 0 0 0 0 0 0 0 0 0
    1.4752 12.6971 -3.7566 H 0 0 0 0 0 0 0 0 0 0 0 0
    0.6685 11.4529 -2.7720 H 0 0 0 0 0 0 0 0 0 0 0 0
    1.9564 12.2035 2.1393 H 0 0 0 0 0 0 0 0 0 0 0 0
    0.4401 13.1335 2.0722 H 0 0 0 0 0 0 0 0 0 0 0 0
    0.4643 11.4318 1.5506 H 0 0 0 0 0 0 0 0 0 0 0 0
  1 2 1 0 0 0 0
  1 3 2 0 0 0 0
  1 18 1 0 0 0 0
  3 4 1 0 0 0 0
  3 22 1 0 0 0 0
  4 5 2 0 0 0 0
  4 17 1 0 0 0 0
  5 6 1 0 0 0 0
  5 7 1 0 0 0 0
  6 18 2 0 0 0 0
  6 23 1 0 0 0 0
  7 8 2 0 0 0 0
  8 9 1 0 0 0 0
  8 17 1 0 0 0 0
  9 10 2 0 0 0 0
  9 16 1 0 0 0 0
 10 11 1 0 0 0 0
 10 15 1 0 0 0 0
 11 12 1 0 0 0 0
 11 13 2 0 0 0 0
 13 14 1 0 0 0 0
 13 24 1 0 0 0 0
 14 16 2 0 0 0 0
 14 25 1 0 0 0 0
 15 26 1 0 0 0 0
 16 27 1 0 0 0 0
 17 28 1 0 0 0 0
 18 19 1 0 0 0 0
 19 20 2 0 0 0 0
 19 21 1 0 0 0 0
 20 29 1 0 0 0 0
 20 30 1 0 0 0 0
 21 31 1 0 0 0 0
 21 32 1 0 0 0 0
 33 12 1 0 0 0 0
 33 34 1 0 0 0 0
 33 35 1 0 0 0 0
 35 36 1 0 0 0 0
 36 37 1 0 0 0 0
 34 38 1 0 0 0 0
 37 38 1 0 0 0 0
 35 39 1 0 0 0 0
 33 40 1 0 0 0 0
 34 41 1 0 0 0 0
 34 42 1 0 0 0 0
 35 43 1 0 0 0 0
 36 44 1 0 0 0 0
 36 45 1 0 0 0 0
 37 46 1 0 0 0 0
 37 47 1 0 0 0 0
 38 48 1 0 0 0 0
 38 49 1 0 0 0 0
 39 50 1 0 0 0 0
 39 51 1 0 0 0 0
 39 52 1 0 0 0 0
M END

$$$$

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