- modeller_usage - salilab.org

Error" Array too small. Increase MAXBND"
by Youbin Tu 27 Oct '04

27 Oct '04

Hi all: Anyone has met such an error " Array too small. Increase MAXBND"? I was trying to build a small ligand into the model, it seems that sth wrong with the process of creating topology. I tried both modeler6vs2 and modeler7v7, unfortunately they gave the same errors. Here is the final part of the log file: *********************************************************************** TOP_________> 135 91 CALL ROUTINE = 'create_topology' TOP_________> 136 106 GENERATE_TOPOLOGY ADD_SEQUENCE = OFF mkilst______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 1 513 4139 4201 0 0 1775 patch_______> segment topology patched using RTF: 1 ; MET ; NTER segments residues atoms bonds angles dihedrals impropers: 1 513 4139 4201 5696 6784 1775 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 1 513 4139 4201 5696 6784 1775 getf____223E> Array too small. Increase MAXBND current maximum, current need: 6948 6949 recover____E> ERROR_STATUS >= STOP_ON_ERROR: 1 1 Dynamically allocated memory at finish [B,kB,MB]: 8307049 8112.353 7.922 Starting time : 2004/10/26 14:20:01.859 Closing time : 2004/10/26 14:20:05.468 Total CPU time [seconds] : 3.28 ********************************************************************* Anyone has some ideas about it? Thanks. youbin

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multiple alignment...
by limnoha 25 Oct '04

25 Oct '04

Hello all... I tried to run my code for multiple alignment. <top file> READ_MODEL FILE = '1ry2.pdb', MODEL_SEGMENT 'FIRST:A''LAST:A' SEQUENCE_TO_ALI ALIGN_CODES = '1ry2A' READ_MODEL FILE = '1pg4.pdb', MODEL_SEGMENT 'FIRST:B''LAST:B' SEQUENCE_TO_ALI ALIGN_CODES = ALIGN_CODES '1ry2A',ADD_SEQUENCE = on READ_MODEL FILE = '1t5d.pdb', MODEL_SEGMENT 'FIRST:X''LAST:X' SEQUENCE_TO_ALI ALIGN_CODES = ALIGN_CODES '1ry2A',ADD_SEQUENCE = on READ_MODEL FILE = '1t5h.pdb', MODEL_SEGMENT 'FIRST:X''LAST:X' SEQUENCE_TO_ALI ALIGN_CODES = ALIGN_CODES '1ry2A',ADD_SEQUENCE = on SET ATOM_FILES = '1ry2' '1pg4' '1t5d' '1t5h' MALIGN3D SET ADD_SEQUENCE = on, ALIGN_BLOCK = NUMB_OF_SEQUENCES READ_ALIGNMENT FILE = 'target.seq', ALIGN_CODES = ALIGN_CODES 'target' ALIGN2D WRITE_ALIGNMENT FILE = 'target.ali', ALIGNMENT_FORMAT = 'PIR' WRITE_ALIGNMENT FILE = 'target.pap', ALIGNMENT_FORMAT = 'PAP' But, my job wasn't termainate. And, it always made the same log file and stopped at the same point. <log file> Date and time of compilation : 09/14/2004 11:06:39 Job starting time (YY/MM/DD HH:MM:SS): 2004/10/23 00:03:24.704 # Sequence alignment of the structurally conserved regions # [average distance and standard deviation are with respect # to the framework (i.e., average structure)] # # N av ds st dv 1ry2A 1ry2A 1ry2A 1ry2A # ============================================= 1 0.585 0.177 A 95 G 43 K 89 K 89 2 0.520 0.238 T 96 K 44 S 90 S 90 # ============================================= 3 0.904 0.201 F 98 I 45 L 93 L 93 # ============================================= 4 0.927 0.182 S 102 I 49 V 109 V 109 # ============================================= 5 0.648 0.243 K 149 T 93 P 155 P 155 # ============================================= 6 1.286 0.094 A 150 A 94 F 157 F 157 # ============================================= 7 1.086 0.362 * I 151 I 95 I 173 I 173 8 1.203 0.241 I 152 I 96 P 174 P 174 # ============================================= 9 0.687 0.125 F 153 W 97 A 177 A 177 # ============================================= 10 1.147 0.112 M 198 M 141 R 181 R 181 11 1.499 0.072 * V 199 V 142 V 182 V 182 # ============================================= 12 1.603 0.195 A 221 G 164 M 185 M 185 # ============================================= 13 1.035 0.235 G 222 G 165 V 189 V 189 # ============================================= 14 0.604 0.191 T 255 L 198 R 192 R 192 15 1.418 0.057 K 256 K 199 H 193 H 193 # ============================================= 16 1.600 0.394 V 272 V 217 R 195 R 195 # ============================================= 17 0.982 0.421 V 274 V 219 D 222 D 222 # ============================================= 18 1.174 0.252 P 314 P 258 E 230 E 230 # ============================================= 19 0.735 0.103 L 318 L 262 A 250 A 250 # ============================================= 20 1.896 0.448 G 322 S 265 L 289 L 289 # ============================================= 21 1.220 0.197 G 325 G 269 Q 294 Q 294 22 1.196 0.192 A 326 K 270 H 295 H 295 23 1.671 0.053 P 327 P 271 L 296 L 296 # ============================================= 24 0.801 0.374 G 361 A 305 G 305 G 305 # ============================================= 25 1.195 0.112 V 372 L 316 T 307 T 307 # ============================================= 26 0.836 0.059 G 388 G 332 F 329 F 329 27 1.111 0.360 T 389 V 333 S 330 S 330 28 1.141 0.216 P 390 P 334 E 331 E 331 # ============================================= 29 0.968 0.251 Y 398 M 342 A 356 A 356 # ============================================= 30 1.430 0.434 I 401 V 345 A 357 A 357 # ============================================= 31 1.501 0.129 T 408 N 352 T 372 T 372 # ============================================= 32 0.657 0.212 R 437 R 381 E 374 E 374 # ============================================= 33 1.114 0.104 G 440 G 384 S 384 S 384 34 1.061 0.137 S 441 S 385 D 385 D 385 # ============================================= 35 1.024 0.321 P 445 P 389 L 398 L 398 # ============================================= 36 0.638 0.207 D 467 D 411 R 400 R 400 # ============================================= 37 1.117 0.411 S 493 S 436 M 404 M 404 # ============================================= 38 1.524 0.844 P 508 D 450 A 424 A 424 39 1.217 0.673 N 509 N 451 P 425 P 425 # ============================================= 40 0.940 0.301 A 524 V 465 E 429 E 429 # ============================================= 41 1.773 0.332 K 563 R 504 V 432 V 432 # ============================================= 42 1.163 0.303 D 564 D 505 V 444 V 444 # ============================================= # Sequence alignment of the structurally conserved regions # [average distance and standard deviation are with respect # to the framework (i.e., average structure)] # # N av ds st dv 1ry2A 1ry2A 1ry2A 1ry2A # ============================================= 1 0.706 0.084 A 95 G 43 K 89 K 89 2 0.693 0.277 T 96 K 44 S 90 S 90 # ============================================= 3 0.982 0.231 F 98 I 45 L 93 L 93 # ============================================= 4 0.595 0.283 S 102 I 49 V 109 V 109 # ============================================= 5 0.896 0.032 K 149 T 93 P 155 P 155 # ============================================= 6 1.152 0.046 A 150 A 94 F 157 F 157 # ============================================= 7 1.021 0.088 * I 151 I 95 I 173 I 173 8 0.926 0.038 I 152 I 96 P 174 P 174 # ============================================= 9 0.619 0.086 F 153 W 97 A 177 A 177 # ============================================= 10 0.929 0.116 M 198 M 141 R 181 R 181 11 1.627 0.065 * V 199 V 142 V 182 V 182 # ============================================= 12 1.365 0.199 A 221 G 164 M 185 M 185 # ============================================= 13 0.840 0.173 G 222 G 165 V 189 V 189 # ============================================= 14 0.537 0.054 T 255 L 198 R 192 R 192 15 1.201 0.041 K 256 K 199 H 193 H 193 # ============================================= 16 1.548 0.190 V 272 V 217 R 195 R 195 # ============================================= 17 0.956 0.153 L 273 I 218 D 222 D 222 # ============================================= 18 1.004 0.175 P 314 P 258 E 230 E 230 # ============================================= 19 0.617 0.067 L 318 L 262 A 250 A 250 # ============================================= 20 0.818 0.094 G 325 G 269 Q 294 Q 294 # ============================================= 21 1.170 0.262 A 326 K 270 L 296 L 296 # ============================================= 22 0.692 0.159 G 361 A 305 G 305 G 305 # ============================================= 23 1.107 0.040 V 372 L 316 T 307 T 307 # ============================================= 24 0.727 0.091 G 388 G 332 F 329 F 329 25 0.677 0.232 T 389 V 333 S 330 S 330 26 0.911 0.197 P 390 P 334 E 331 E 331 # ============================================= 27 0.373 0.111 Y 398 M 342 A 356 A 356 # ============================================= 28 1.333 0.184 I 401 V 345 A 357 A 357 # ============================================= 29 1.131 0.064 T 408 N 352 T 372 T 372 # ============================================= 30 1.428 0.154 S 435 S 379 A 373 A 373 # ============================================= 31 0.724 0.277 R 437 R 381 E 374 E 374 # ============================================= 32 1.053 0.062 G 440 G 384 S 384 S 384 33 0.969 0.111 S 441 S 385 D 385 D 385 # ============================================= 34 1.728 0.101 E 444 E 388 I 397 I 397 35 0.827 0.113 P 445 P 389 L 398 L 398 # ============================================= 36 0.442 0.180 D 467 D 411 R 400 R 400 # ============================================= 37 1.048 0.082 S 493 S 436 M 404 M 404 # ============================================= 38 1.158 0.402 P 508 N 451 A 424 A 424 # ============================================= 39 1.107 0.657 E 512 G 453 G 426 G 426 # ============================================= 40 0.713 0.102 A 524 V 465 E 429 E 429 # ============================================= 41 1.767 0.252 K 563 R 504 V 432 V 432 # ============================================= 42 0.397 0.229 D 566 D 507 L 435 L 435 # ============================================= # Sequence alignment of the structurally conserved regions # [average distance and standard deviation are with respect # to the framework (i.e., average structure)] # # N av ds st dv 1ry2A 1ry2A 1ry2A 1ry2A # ============================================= 1 0.764 0.077 A 95 G 43 K 89 K 89 2 0.723 0.284 T 96 K 44 S 90 S 90 # ============================================= 3 0.989 0.125 F 98 I 45 L 93 L 93 # ============================================= 4 0.586 0.237 S 102 I 49 V 109 V 109 # ============================================= 5 0.968 0.053 K 149 T 93 P 155 P 155 # ============================================= 6 1.242 0.038 A 150 A 94 F 157 F 157 # ============================================= 7 0.976 0.067 * I 151 I 95 I 173 I 173 8 0.852 0.041 I 152 I 96 P 174 P 174 # ============================================= 9 0.808 0.096 F 153 W 97 A 177 A 177 # ============================================= 10 0.820 0.129 M 198 M 141 R 181 R 181 # ============================================= 11 1.204 0.208 A 221 G 164 M 185 M 185 # ============================================= 12 0.918 0.216 G 222 G 165 V 189 V 189 # ============================================= 13 0.746 0.066 T 255 L 198 R 192 R 192 14 1.117 0.062 K 256 K 199 H 193 H 193 # ============================================= 15 1.447 0.158 V 272 V 217 R 195 R 195 # ============================================= 16 0.764 0.146 L 273 I 218 D 222 D 222 # ============================================= 17 1.130 0.160 P 314 P 258 E 230 E 230 # ============================================= 18 0.592 0.048 L 318 L 262 A 250 A 250 # ============================================= 19 0.713 0.133 G 325 G 269 Q 294 Q 294 # ============================================= 20 1.162 0.358 A 326 K 270 L 296 L 296 # ============================================= 21 0.755 0.173 G 361 A 305 G 305 G 305 # ============================================= 22 1.029 0.038 V 372 L 316 T 307 T 307 # ============================================= 23 0.697 0.088 G 388 G 332 F 329 F 329 24 0.516 0.222 T 389 V 333 S 330 S 330 25 0.803 0.290 P 390 P 334 E 331 E 331 # ============================================= 26 0.399 0.067 Y 398 M 342 A 356 A 356 # ============================================= 27 1.485 0.185 I 401 V 345 A 357 A 357 # ============================================= 28 0.983 0.083 T 408 N 352 T 372 T 372 # ============================================= 29 1.326 0.211 S 435 S 379 A 373 A 373 # ============================================= 30 0.837 0.266 R 437 R 381 E 374 E 374 # ============================================= 31 1.013 0.090 G 440 G 384 S 384 S 384 32 0.911 0.144 S 441 S 385 D 385 D 385 # ============================================= 33 1.568 0.072 E 444 E 388 I 397 I 397 34 0.663 0.120 P 445 P 389 L 398 L 398 # ============================================= 35 0.501 0.235 D 467 D 411 R 400 R 400 # ============================================= 36 0.950 0.117 S 493 S 436 Please solve my problem...

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error on 'special_patches' routine for PATCH S-S bonds
by Dr. Daniel James White PhD 25 Oct '04

25 Oct '04

Hi Modellers, I get a "command not recognized" error, see log below when trying to use the 'special_patches' routine, to tell modeller to make 2 S-S bonds in a loop I am modelling, I can't see any error in my top file or alignment, I used the code directly from the manual FAQ number 6, define additional disulphides not in template, with appropriate changes, see top file below. any ideas what I am doing wrong? cheers Dan top file: # Homology modelling by the MODELLER TOP routine 'model'. INCLUDE # Include the predefined TOP routines SET OUTPUT_CONTROL = 1 1 1 1 1 # uncomment to produce a large log file SET ALNFILE = 'loop1.ali' # alignment filename SET KNOWNS = '4DPV' # codes of the templates SET SEQUENCE = 'lop1' # code of the target SET ATOM_FILES_DIRECTORY = './:../atom_files' # directories for input atom files SET STARTING_MODEL= 1 # index of the first model SET ENDING_MODEL = 1 # index of the last model # (determines how many models to calculate) CALL ROUTINE = 'model' STOP # Redefine the special_patches routine to include the additional disulfides # (this routine is empty by default): SUBROUTINE ROUTINE = 'special_patches' # A disulfide between residues 226 and 234 in chain A: PATCH RESIDUE_TYPE = 'DISU', RESIDUE_IDS = '226:A' '234:A' # A disulfide between residues 228 and 232 in chain A: PATCH RESIDUE_TYPE = 'DISU', RESIDUE_IDS = '228:A' '232:A' RETURN END_SUBROUTINE log file: Kind, OS, HostName, Kernel, Processor: 4, Linux modeling.bio.jyu.fi 2.6.8-1.521 i686 Date and time of compilation : 09/14/2004 11:06:39 Job starting time (YY/MM/DD HH:MM:SS): 2004/10/12 15:04:54.106 rdactio_534E> Command not recognized: recover____E> ERROR_STATUS >= STOP_ON_ERROR: 1 1 Dynamically allocated memory at finish [B,kB,MB]: 56755 55.425 0.054 Starting time : 2004/10/12 15:04:54.106 Closing time : 2004/10/12 15:04:55.092 Total CPU time [seconds] : 0.94 ali file: >P1;4DPV-CPVVP-withDNAZ structure:4DPV:22 :Z:593 :Z:::: GSGNGSGGGGGGGSGGVGISTGTFNNQTEFKFLENGWVEITANSSRLVHLNMPESENYRR VVVNNMDKTAVNGNMALDDIHAQIVTPWSLVDANAWGVWFNPGDWQLIVNTMSELHLVSF EQEIFNVVLKTVSE----PPTKVYNNDLTASLMVALDSNNTMPFTPAAMRSETLGFYPWK PTIPTPWRYYFQWDRTLIPSHTGT---------SGTPTNIYHGTDPDDVQFYTIENSVPVHLLRTGDEF ATGTFFFDCKPCRLTHTWQTNRALGLPPFLNSLPQSEGATNFGDIGVQQDKRRGVTQMGN TNYITEATIMRPAEVGYSAPYYSFEASTQGPFKTPIAAGRGGAQTDENQAADGNPRYAFG RQHGQKTTTTGETPERFTYIAHQDTGRYPEGDWIQNINFNLPVTNDNVLLPTDPIGGKTG INYTNIFNTYGPLTALNNVPPVYPNGQIWDKEFDTDLKPRLHVNAPFVCQNNCPGQLFVK VAPNLTNEYDPDASANMSRIVTYSDFWWKGKLVFKAKLRASHTWNPIQQMSINVDNQFNY VPSNIGGMKIVYEKSQLAPRKLY* >P1;COAT_PAVC2_VP2 sequence:lop1:22 :A:593 : :A::: GSGNGSGGGGGGGSGGVGISTGTFNNQTEFKFLENGWVYITANSSRLVHLNMPESENYRR VVVNNMDKTAVNGNMALDDIHAEIVTPWSLVDANAWGVWFNPGDWQLIVNTMSELHLVSF EQEIFNVVLKTVSESATQPPTKVYNNDLTASLMVALDSNNTMPFTPAAMRSETLGFYPWK PTIPTPWRYYFQWDRTLIPSHTGTCDCRGDCFCSGTPTNIYHGTDPDDVQFYTIENSVPVHLLRTGDEF ATGTFFFDCKPCRLTHTWQTNRALGLPPFLNSLPQSEGATNFGDIGVQQDKRRGVTQMGN TNYITEATIMRPAEVGYSAPYYSFEASTQGPFKTPIAAGRGGAQTDENQAADGNPRYAFG RQHGKKTTTTGETPERFTYIAHQDTGRYPEGDWIQNINFNLPVTNDNVLLPTDPIGGKTG INYTNIFNTYGPLTALNNVPPVYPNGQIWDKEFDTDLKPRLHVNAPFVCQNNCPGQLFVK VAPNLTNQYDPDASANMSRIVTYSDFWWKGKLVFKAKLRASHTWNPIQQMSINVDNQFNY VPSNIGGMKIVYEKSQLAPRKLY* Dr. Daniel James White BSc. (Hons.) PhD Cell Biology, Ambiotica C242 Department of biological and environmental science PO Box 35 University of Jyväskylä Jyväskylä FIN 40014 Finland +358 14 260 4183 (work) +358 468102840 (mobile) http://www.chalkie.org.uk dan(a)chalkie.org.uk white(a)cc.jyu.fi

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where can I get file.crv file.cav by write_date
by Shu-Qun Liu 21 Oct '04

21 Oct '04

Dear Modeller Users and Developers, The WRITE_DATA command can write the selected types of data (such as PSA DIH NGH SSM CRV CAV CROSS-SECTIONS) about the MODEL to a corresponding file. The example script write_data.top in the path 'modeller7v7/example/commands' is: # Example for: WRITE_DATA # This will calculate solvent accessibility, dihedral angles, and # residue-residue neighbors for a structure in the PDB file. SET OUTPUT_CONTROL = 1 1 1 1 1 # Get topology library for radii and the model without waters and # HETATMs: READ_TOPOLOGY FILE = '$(LIB)/top_heav.lib' SET HETATM_IO = off, WATER_IO = off READ_MODEL FILE = '1fas' # Calculate residue solvent accessibilities, dihedral angles, and # residue-residue neighbors: SET RADII_FACTOR = 1.0 # The default is 0.82 (for soft-sphere restraints) WRITE_DATA FILE = '1fas', OUTPUT = 'PSA DIH NGH SSM CRV' After I run this script, I can get corresponding files: 1fas.dih 1fas.ngh 1fas.psa 1fas.sol 1fas.ssm. However, when I changed the last line "WRITE_DATA FILE = '1fas', OUTPUT = 'PSA DIH NGH SSM CRV'" into "WRITE_DATA FILE = '1fas', OUTPUT = 'ALL'" or "WRITE_DATA FILE = '1fas', OUTPUT = 'CRV CAV CROSS-SECTIONS'", I can not find 1fas.crv, 1fas.cav in the ouput directory. And there is no information on writing 1fas.crv and 1fas.cav in write_data.log file. Where can I get these two files or information about mainchain curvatures and protein internal cavity volums? is it a bug? Best regards Shuqun Liu

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hetatms placed far away from the backbone
by Michael Knoll 20 Oct '04

20 Oct '04

Dear Modellers, I'm trying to model a ZN-containing (two zn ions) protein with modeller6v2. I used : 'SET HETATM_IO = on' in the .top file and the following syntax in the .ali file : ------------------------------------------ >P1;template structure:template:2:A: :A: : : : ANHD...VGN---LYPE-/zz* >P1;target sequence:target: : : : : : : : ANHD...VGNPL-LYR-G/zz* --------------------------------------------- I renamed the ZN in the template pdb file to ZN2 and the residue numbers are continuous. The model building results in a model where the overall structure of the model looks almost good, but the zn atoms are PLACED FAR AWAY from the model backbone. I tried to solve this problem many times without success so far. So, I would be very happy if anybody could help me. Thanks to all in advance, Michael ******************************************** Michael Knoll email : michael.knoll(a)itb.uni-stuttgart.de ********************************************

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Modeller stopped with no specific error message
by 서주현 20 Oct '04

20 Oct '04

3 2

calling subroutine defsym
by amc 20 Oct '04

20 Oct '04

Dear modellers, I am modelling a homotetramer protein and curious when or by what the subroutine 'defsym' is called. Cheers, Han

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Alignment file.
by bcur001＠ec.auckland.ac.nz 13 Oct '04

13 Oct '04

I'm doing something wrong, I'm a novice though, so I know what what. I'm using a fairly simple TOP script to generate a model a nitroreductase. I've used blast on NCBI to find a simialr protein to the one I have the pdb model for. The blast results look like this : Query: 1 MDIISVALKRHSTKAFDASKKLTPEQAEQIKTLLQYSPSSTNSQPWHFIVASTEEGKARV 60 MDIISVALKRHSTKAFDASKKLT E+AE+IKTLLQYSPSSTNSQPWHFIVASTEEGKARV Sbjct: 1 MDIISVALKRHSTKAFDASKKLTAEEAEKIKTLLQYSPSSTNSQPWHFIVASTEEGKARV 60 Query: 61 AKSAAGNYVFNERKMLDASHVVVFCAKTAMDDVWLKLVVDQEDADGRFATPEAKAANDKG 120 AKSAAG YVFNERKMLDASHVVVFCAKTAMDD WL+ VVDQE+ADGRF TPEAKAAN KG Sbjct: 61 AKSAAGTYVFNERKMLDASHVVVFCAKTAMDDAWLERVVDQEEADGRFNTPEAKAANHKG 120 Query: 121 RKFFADMHRKDLHDDAEWMAKQVYLNVGNFXXXXXXXXXXXXPIEGFDAAILDAEFGLKE 180 R +FADMHR DL DD +WMAKQVYLNVGNF PIEGFDAAILD EFGLKE Sbjct: 121 RTYFADMHRVDLKDDDQWMAKQVYLNVGNFLLGVGAMGLDAVPIEGFDAAILDEEFGLKE 180 Query: 181 KGYTSLVVVPVGHHSVEDFNATLPKSRLPQNITLTE 216 KG+TSLVVVPVGHHSVEDFNATLPKSRLP + +TE Sbjct: 181 KGFTSLVVVPVGHHSVEDFNATLPKSRLPLSTIVTE 216 How do I then transform this into a successful alignment file? My attempt looks something like this: >P1;1OO5 structureX:1OO5: 2 :A: 217 :D:undefined:undefined:-1.00:-1.00 mdiisvalkrhstkafdaskkltpeqaeqiktllqyspsstnsqpwhfivasteegkarvaksaagnyvfnerkml dashvvvfcaktamddvwlklvvdqedadgrfatpeakaandkgrkffadmhrkdlhddaewmakqvylnvgnfll gvaalgldavpiegfdaaildaefglkekgytslvvvpvghhsvedfnatlpksrlpq nitltev* >P1;1NEC sequence:1NEC: 2 :A: 216 :D:undefined:undefined:-1.00:-1.00 DIISVALKRHSTKAFDASKKLTAEEAEKIKTLLQYSPSSTNSQPWHFIVASTEEGKARVAKSAAGTYVFNERKML DASHVVVFCAKTAMDDAWLERVVDQEEADGRFNTPEAKAANHKGRTYFADMHRVDLKDDDQWMAKQVYLNVGNFL LGVGAMGLDAVPIEGFDAAILDEEFGLKEKGFTSLVVVPVGHHSVEDFNATLPKSRLPLSTIVTE* I've basically taken the Query sequence (1OO5) which I have the pdb file for and placed it in the sequence section, then taken the result sequence which has been matched to it (1NEC) and placed it in the second position of the alignment file with the sequence label. However, when I run it, in my mod.log file, I'm getting the error: Dynamically allocated memory at amaxseq [B,kB,MB]: 2205269 2153.583 2.103 openf5__224_> Open 11 OLD SEQUENTIAL 1OO5.ali Dynamically allocated memory at amaxbnd [B,kB,MB]: 5377489 5251.454 5.128 openf5__224_> Open 11 OLD SEQUENTIAL 1OO5.ali read_al_375E> Unknown residue type,position,sequence: m 1 1 recover____E> ERROR_STATUS >= STOP_ON_ERROR: 1 1 As far as I can gatherThis means that it doesn't like the residue at position one. I don't however know what it doesn't like about the residue at that position. Am I creating the alignment file in the wrong manner? Is there something else wrong? In case it of any use, the top file looks like: INCLUDE # Include the predefined TOP routines SET OUTPUT_CONTROL = 1 1 1 1 1 # uncomment to produce a large log file SET ALNFILE = '1ICV.ali' # alignment filename SET KNOWNS = '1ICV' # codes of the templates SET SEQUENCE = '1NEC' # code of the target # SET HYDROGEN_IO = on SET HETATM_IO = on SET ATOM_FILES_DIRECTORY = '../pdb' # directories for input atom files SET STARTING_MODEL= 1 # index of the first model SET ENDING_MODEL = 10 # index of the last model # (determines how many models to calculate) SET PDB_EXT = '.modlr.pdb' SET MD_LEVEL = 'refine_5' SET LIBRARY_SCHEDULE = 1 CALL ROUTINE = 'model Thanks. Ben.

2 1

bumps in model
by Marc Gasser 13 Oct '04

13 Oct '04

dear Modellers, I used MUTATE_MODEL to mutate ALA into ILE. now the ILE bumps into another residue. turning the dihedral of the ILE sidechain manually in a viewer will solve this. but I want to include an automatic minimization process in the mutate.top script, which will do it for me. In the FAQ section I saw the question 2. which describes a similar problem, it refers to examples/tutorial-model/model-segment.top . but it's not so clear to me how to merge the mutate.top and the model-segment.top in one both_steps.top, does it really need an alignment for doing this optimization of one residue? thank you for good tips. marc

1 1

PDB updates for Modeller
by Bruno Afonso 07 Oct '04

07 Oct '04

Dear modeller hackers :), I'm trying to use modeller to find good PDB templates and there is at least one structure that is missing from modeller's database, which is good since it was deposited Jun 2003 in PDB, released in august. Could it be because it is 3.3 A? Since I know this PDB is probably a good model and it won't come up in seq_search I was wondering how I could manually update CHAINS_all.seq or create my own sequence database. best, BA ps: I found in the archives a person asking a similar question regarding a PDB database update but no script or url was given to get a newer version, or without resolution cut-off. :-) -- Bruno Afonso http://brunoafonso.net http://dequim.ist.utl.pt/~bruno/sciTocs/ - Bruno's SciTocs! http://freebsd-pt.org/forum/ - Portuguese FreeBSD forum

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