Dear Amber Users,
I have two Zn coordination systems in my protein. I cleaned my PDB and
executed the following commands in leap.
tleap -s -f $AMBERHOME/dat/leap/cmd/leaprc.ff14SB
addAtomTypes { { "ZN" "Zn" "sp3" } { "S3" "S" "sp3" } }
loadoff atomic_ions.lib
loadamberparams frcmod.ions1lsm_hfe_tip3p
loadamberprep ZAFF.prep
loadamberparams ZAFF.frcmod
mol = loadpdb wt_clean2.pdb
bond mol.1410.ZN mol.888.SG
bond mol.1410.ZN mol.895.SG
bond mol.1410.ZN mol.898.SG
bond mol.1410.ZN mol.814.SG
As I execute the bond command I get the following errors for each bond
command.
bond: Argument #2 is type String must be of type: [atom]
usage: bond <atom1> <atom2> [order]
Whereas when I use the same bond command for the other Zn, it doesn't
throw any error.
bond mol.1409.ZN mol.70.SG
bond mol.1409.ZN mol.72.SG
bond mol.1409.ZN mol.85.SG
bond mol.1409.ZN mol.88.SG
There were no errors thrown for these second set of bond commands.
Can someone help me why the leap is throwing the error, even though I have
used pointer pointing only atoms in the command?
These are my Zn coordination residues-
ATOM 1147 N CY1 70 128.847 145.112 153.017 -0.4157 1.5500
N
ATOM 1148 H CY1 70 128.432 144.515 152.323 0.2719 1.3000
H
ATOM 1149 CA CY1 70 128.266 145.150 154.346 0.0213 1.7000
C
ATOM 1150 HA CY1 70 128.217 146.179 154.676 0.1124 1.2000
H
ATOM 1151 CB CY1 70 126.845 144.595 154.334 -0.1231 1.7000
C
ATOM 1152 HB2 CY1 70 126.230 145.220 153.686 0.1112 1.2000
H
ATOM 1153 HB3 CY1 70 126.867 143.586 153.920 0.1112 1.2000
H
ATOM 1154 SG CY1 70 126.091 144.526 155.964 -0.3119 1.8000
S
ATOM 1155 HG CY1 70 125.916 145.843 156.099 0.1933 1.2000
H
ATOM 1156 C CY1 70 129.108 144.348 155.329 0.5973 1.7000
C
ATOM 1157 O CY1 70 130.051 143.643 154.962 -0.5679 1.5000
O
ATOM 1177 N CY1 72 127.753 142.043 157.573 -0.4157 1.5500
N
ATOM 1178 H CY1 72 127.100 142.781 157.354 0.2719 1.3000
H
ATOM 1179 CA CY1 72 127.278 140.670 157.691 0.0213 1.7000
C
ATOM 1180 HA CY1 72 127.744 140.206 158.562 0.1124 1.2000
H
ATOM 1181 CB CY1 72 125.770 140.648 157.906 -0.1231 1.7000
C
ATOM 1182 HB2 CY1 72 125.478 139.618 158.113 0.1112 1.2000
H
ATOM 1183 HB3 CY1 72 125.511 141.249 158.775 0.1112 1.2000
H
ATOM 1184 SG CY1 72 124.841 141.209 156.480 -0.3119 1.8000
S
ATOM 1185 HG CY1 72 125.072 142.514 156.657 0.1933 1.2000
H
ATOM 1186 C CY1 72 127.645 139.855 156.460 0.5973 1.7000
C
ATOM 1187 O CY1 72 128.032 138.688 156.573 -0.5679 1.5000
O
ATOM 1408 N CY1 85 121.747 147.502 155.149 -0.4157 1.5500
N
ATOM 1409 H CY1 85 122.695 147.802 155.321 0.2719 1.3000
H
ATOM 1410 CA CY1 85 121.334 146.162 155.535 0.0213 1.7000
C
ATOM 1411 HA CY1 85 120.732 145.733 154.731 0.1124 1.2000
H
ATOM 1412 CB CY1 85 122.546 145.266 155.738 -0.1231 1.7000
C
ATOM 1413 HB2 CY1 85 123.066 145.190 154.784 0.1112 1.2000
H
ATOM 1414 HB3 CY1 85 123.236 145.725 156.436 0.1112 1.2000
H
ATOM 1415 SG CY1 85 122.134 143.609 156.281 -0.3119 1.8000
S
ATOM 1416 HG CY1 85 121.224 143.386 155.333 0.1933 1.2000
H
ATOM 1417 C CY1 85 120.496 146.218 156.800 0.5973 1.7000
C
ATOM 1418 O CY1 85 120.856 146.888 157.771 -0.5679 1.5000
O
ATOM 1456 N CY1 88 122.152 144.186 160.031 -0.4157 1.5500
N
ATOM 1457 H CY1 88 122.245 144.135 159.027 0.2719 1.3000
H
ATOM 1458 CA CY1 88 123.047 145.084 160.746 0.0213 1.7000
C
ATOM 1459 HA CY1 88 122.587 145.403 161.682 0.1124 1.2000
H
ATOM 1460 CB CY1 88 124.373 144.431 161.069 -0.1231 1.7000
C
ATOM 1461 HB2 CY1 88 124.990 145.154 161.604 0.1112 1.2000
H
ATOM 1462 HB3 CY1 88 124.191 143.590 161.739 0.1112 1.2000
H
ATOM 1463 SG CY1 88 125.318 143.834 159.645 -0.3119 1.8000
S
ATOM 1464 HG CY1 88 125.259 144.970 158.949 0.1933 1.2000
H
ATOM 1465 C CY1 88 123.259 146.307 159.873 0.5973 1.7000
C
ATOM 1466 O CY1 88 123.516 146.172 158.676 -0.5679 1.5000
O
ATOM 12993 N CY1 814 152.534 203.432 142.773 -0.4157 1.5500
N
ATOM 12994 H CY1 814 153.509 203.476 143.029 0.2719 1.3000
H
ATOM 12995 CA CY1 814 151.556 204.186 143.544 0.0213 1.7000
C
ATOM 12996 HA CY1 814 150.550 203.820 143.332 0.1124 1.2000
H
ATOM 12997 CB CY1 814 151.783 203.997 145.043 -0.1231 1.7000
C
ATOM 12998 HB2 CY1 814 150.916 204.406 145.558 0.1112 1.2000
H
ATOM 12999 HB3 CY1 814 151.822 202.930 145.259 0.1112 1.2000
H
ATOM 13000 SG CY1 814 153.271 204.791 145.682 -0.3119 1.8000
S
ATOM 13001 HG CY1 814 152.727 206.005 145.804 0.1933 1.2000
H
ATOM 13002 C CY1 814 151.605 205.667 143.209 0.5973 1.7000
C
ATOM 13003 O CY1 814 150.562 206.330 143.186 -0.5679 1.5000
O
ATOM 14131 N CY1 888 155.373 203.452 151.566 -0.4157 1.5500
N
ATOM 14132 H CY1 888 155.673 202.619 152.051 0.2719 1.3000
H
ATOM 14133 CA CY1 888 154.598 203.319 150.345 0.0213 1.7000
C
ATOM 14134 HA CY1 888 154.984 204.016 149.599 0.1124 1.2000
H
ATOM 14135 CB CY1 888 154.714 201.910 149.774 -0.1231 1.7000
C
ATOM 14136 HB2 CY1 888 155.764 201.695 149.574 0.1112 1.2000
H
ATOM 14137 HB3 CY1 888 154.353 201.196 150.516 0.1112 1.2000
H
ATOM 14138 SG CY1 888 153.778 201.677 148.251 -0.3119 1.8000
S
ATOM 14139 HG CY1 888 154.477 202.538 147.509 0.1933 1.2000
H
ATOM 14140 C CY1 888 153.133 203.649 150.597 0.5973 1.7000
C
ATOM 14141 O CY1 888 152.695 203.855 151.730 -0.5679 1.5000
O
ATOM 14223 N CY1 895 154.320 198.655 145.938 -0.4157 1.5500
N
ATOM 14224 H CY1 895 154.150 199.456 146.529 0.2719 1.3000
H
ATOM 14225 CA CY1 895 154.345 198.834 144.494 0.0213 1.7000
C
ATOM 14226 HA CY1 895 153.750 198.039 144.045 0.1124 1.2000
H
ATOM 14227 CB CY1 895 153.705 200.159 144.095 -0.1231 1.7000
C
ATOM 14228 HB2 CY1 895 153.678 200.208 143.006 0.1112 1.2000
H
ATOM 14229 HB3 CY1 895 152.672 200.168 144.434 0.1112 1.2000
H
ATOM 14230 SG CY1 895 154.521 201.612 144.691 -0.3119 1.8000
S
ATOM 14231 HG CY1 895 153.409 202.217 145.121 0.1933 1.2000
H
ATOM 14232 C CY1 895 155.771 198.735 143.975 0.5973 1.7000
C
ATOM 14233 O CY1 895 156.713 199.175 144.638 -0.5679 1.5000
O
ATOM 14261 N CY1 898 158.440 201.434 143.766 -0.4157 1.5500
N
ATOM 14262 H CY1 898 157.722 200.723 143.798 0.2719 1.3000
H
ATOM 14263 CA CY1 898 158.934 201.971 145.027 0.0213 1.7000
C
ATOM 14264 HA CY1 898 159.426 202.930 144.856 0.1124 1.2000
H
ATOM 14265 CB CY1 898 157.763 202.222 145.971 -0.1231 1.7000
C
ATOM 14266 HB2 CY1 898 157.014 202.794 145.444 0.1112 1.2000
H
ATOM 14267 HB3 CY1 898 157.309 201.257 146.201 0.1112 1.2000
H
ATOM 14268 SG CY1 898 158.124 203.024 147.533 -0.3119 1.8000
S
ATOM 14269 HG CY1 898 159.108 202.200 147.893 0.1933 1.2000
H
ATOM 14270 C CY1 898 159.938 201.034 145.679 0.5973 1.7000
C
ATOM 14271 O CY1 898 160.746 201.465 146.506 -0.5679 1.5000
O
HETATM22013 ZN ZN1 1408 124.407 143.482 157.414 1.00 0.00
Zn
HETATM22014 ZN ZN1 1409 155.341 202.836 146.737 1.00 0.00
Zn
Thank you,
Aravind R
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Tue Jun 05 2018 - 22:30:01 PDT
