Dear Bill,
Thank you for the suggestion. The numbering for residues were changed.
Since I had used pdb4amber to clean the pdb, the thought it would not be
numbering problem. It worked now.
Thank you,
Aravind R
> Note that the 'Argument #2' residues that succeed are in residue numbers
> [70..88], however the ones that don't are in the 800's. The higher any
> number goes, the more chance of the unexpected. In this case, if you
> haven't tried, I suggest doing a savepdb, and checking that the residue
> numbers are still numbered as you expect.
>
> Bill
>
> On 6/5/18 10:06 PM, Aravind Ravichandran wrote:
>> 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
>>
>>
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Received on Tue Jun 05 2018 - 23:00:02 PDT
