
PFRMAT FRV1
REMARK ========================================================================
REMARK Fri Jul 19 16:29:18 1996
REMARK This software is guaranteed 100% free of any Biosym, MSI,
REMARK Oxford Molecular or other corporate influence.
REMARK ========================================================================
AUTHOR 8076-4866-8089 Thomas Huber, Chris Dyer, Tian-Xiong Lu and Andrew Torda
AUTHOR 8076-4866-8089 Research School of Chemistry
AUTHOR 8076-4866-8089 Australian National University
AUTHOR 8076-4866-8089 Canberra, ACT 0200
AUTHOR 8076-4866-8089 Australia
AUTHOR 8076-4866-8089 Thomas.Huber@anu.edu.au, dyer@rsc.anu.edu.au,
AUTHOR 8076-4866-8089 lu_t@rsc.anu.edu.au, Andrew.Torda@anu.edu.au
AUTHOR 8076-4866-8089 http://rsc.anu.edu.au/~torda, fax: +61-6-249 0750
REMARK ========================================================================
SEQRES T0014 MKTVTVKNLIIGEGMPKIIVSLMGRDINSVKAEALAYREATFDILEWRVDHFMDIASTQS
SEQRES T0014 VLTAARVIRDAMPDIPLLFTFRSAKEGGEQTITTQHYLTLNRAAIDSGLVDMIDLELFTG
SEQRES T0014 DADVKATVDYAHAHNVYVVMSNHDFHQTPSAEEMVSRLRKMQALGADIPKIAVMPQSKHD
SEQRES T0014 VLTLLTATLEMQQHYADRPVITMSMAKEGVISRLAGEVFGSAATFGAVKQASAPGQIAVN
SEQRES T0014 DLRSVLMILHNA
REMARK ========================================================================
TSCORE T0014 0  0.10    1CTT _ 0
TSCORE T0014 0  0.10    2MNR _ 0
TSCORE T0014 0  0.10    1BNH _ 0
TSCORE T0014 0  0.10    1IVD _ 0
TSCORE T0014 0  0.10    1IRK _ 0
TSCORE T0014 0  0.10    1PPO _ 0
TSCORE T0014 0  0.10    1NIP A 0
TSCORE T0014 0  0.10    1WHT A 0
TSCORE T0014 0  0.10    1FCD A 0
TSCORE T0014 0  0.10    1LCP A 0
TSCORE T0014 0  0.00    1ARB _ 0
TSCORE T0014 0  0.00    1GPH 1 0
TSCORE T0014 0  0.00    2ACT _ 0
TSCORE T0014 0  0.00    1THM _ 0
TSCORE T0014 0  0.00    1SCU A 0
TSCORE T0014 0  0.00    1PKM _ 0
TSCORE T0014 0  0.00    3AAH A 0
TSCORE T0014 0  0.00    1PRH A 0
TSCORE T0014 0  0.00    1KLN A 0
TSCORE T0014 0  0.00    3PTE _ 0
TSCORE T0014 0  0.00    1ST3 _ 0
TSCORE T0014 0  0.00    121P _ 0
TSCORE T0014 0  0.00    2TMD A 0
TSCORE T0014 0  0.00    1DIH _ 0
TSCORE T0014 0  0.00    1ALI A 0
TSCORE T0014 0  0.00    1BUC A 0
TSCORE T0014 0  0.00    1OYC _ 0
TSCORE T0014 0  0.00    1HTI A 0
TSCORE T0014 0  0.00    2LDX _ 0
TSCORE T0014 0  0.00    1MEE A 0
TSCORE T0014 0  0.00    1TRY _ 0
TSCORE T0014 0  0.00    1BMT A 0
TSCORE T0014 0  0.00    1SUP _ 0
TSCORE T0014 0  0.00    1ALD _ 0
TSCORE T0014 0  0.00    1BQL H 0
TSCORE T0014 0  0.00    1PII _ 0
TSCORE T0014 0  0.00    2CMD _ 0
TSCORE T0014 0  0.00    1INV _ 0
TSCORE T0014 0  0.00    2CHR _ 0
TSCORE T0014 0  0.00    1AMY _ 0
TSCORE T0014 0  0.00    1TIS _ 0
TSCORE T0014 0  0.00    1GEC E 0
TSCORE T0014 0  0.00    1TRE A 0
TSCORE T0014 0  0.00    2CTS _ 0
TSCORE T0014 0  0.00    1HJR A 0
TSCORE T0014 0  0.00    1LDM _ 0
TSCORE T0014 0  0.00    1HTB A 0
TSCORE T0014 0  0.00    2PRK _ 0
TSCORE T0014 0  0.00    1MLD A 0
TSCORE T0014 0  0.00    1FNC _ 0
TSCORE T0014 0  0.00    1ENY _ 0
TSCORE T0014 0  0.00    1TAH A 0
TSCORE T0014 0  0.00    9LDT A 0
TSCORE T0014 0  0.00    1MAT _ 0
TSCORE T0014 0  0.00    1MAM H 0
TSCORE T0014 0  0.00    1DXI A 0
TSCORE T0014 0  0.00    1FRG H 0
TSCORE T0014 0  0.00    2BBV C 0
TSCORE T0014 0  0.00    1CSE E 0
TSCORE T0014 0  0.00    1SBP _ 0
TSCORE T0014 0  0.00    1NSC A 0
TSCORE T0014 0  0.00    2MCG 1 0
TSCORE T0014 0  0.00    1PKN _ 0
TSCORE T0014 0  0.00    1ACK _ 0
TSCORE T0014 0  0.00    1LLD A 0
TSCORE T0014 0  0.00    1PTA _ 0
TSCORE T0014 0  0.00    1PDZ _ 0
TSCORE T0014 0  0.00    1PNR A 0
TSCORE T0014 0  0.00    1PRR _ 0
TSCORE T0014 0  0.00    1QOR A 0
TSCORE T0014 0  0.00    1NAR _ 0
TSCORE T0014 0  0.00    1GAL _ 0
TSCORE T0014 0  0.00    1CLC _ 0
TSCORE T0014 0  0.00    1GCA _ 0
TSCORE T0014 0  0.00    1MCP L 0
TSCORE T0014 0  0.00    1NHP _ 0
TSCORE T0014 0  0.00    3BLM _ 0
TSCORE T0014 0  0.00    1DLC _ 0
TSCORE T0014 0  0.00    1ASZ A 0
TSCORE T0014 0  0.00    1NNT _ 0
TSCORE T0014 0  0.00    1TML _ 0
TSCORE T0014 0  0.00    1BBD L 0
TSCORE T0014 0  0.00    1GES A 0
TSCORE T0014 0  0.00    2ALP _ 0
TSCORE T0014 0  0.00    1XYL A 0
TSCORE T0014 0  0.00    1R1A 2 0
TSCORE T0014 0  0.00    1PRT F 0
TSCORE T0014 0  0.00    1MBS _ 0
TSCORE T0014 0  0.00    1BW4 _ 0
TSCORE T0014 0  0.00    1RTC _ 0
TSCORE T0014 0  0.00    1DCT A 0
TSCORE T0014 0  0.00    3ECA A 0
TSCORE T0014 0  0.00    4XIS _ 0
TSCORE T0014 0  0.00    1PYP _ 0
TSCORE T0014 0  0.00    1IBG H 0
TSCORE T0014 0  0.00    1INP _ 0
TSCORE T0014 0  0.00    1FAI H 0
TSCORE T0014 0  0.00    1PRT C 0
TSCORE T0014 0  0.00    1CYG _ 0
TSCORE T0014 0  0.00    1DFB L 0
TSCORE T0014 0  0.00    3PGK _ 0
TSCORE T0014 0  0.00    1MNP _ 0
TSCORE T0014 0  0.00    1HDA B 0
TSCORE T0014 0  0.00    1OVA B 0
TSCORE T0014 0  0.00    2MHB B 0
TSCORE T0014 0  0.00    3PMG A 0
TSCORE T0014 0  0.00    1ERI A 0
TSCORE T0014 0  0.00    7AAT A 0
TSCORE T0014 0  0.00    1HSB A 0
TSCORE T0014 0  0.00    1UDG _ 0
TSCORE T0014 0  0.00    2RMC A 0
TSCORE T0014 0  0.00    3GLY _ 0
TSCORE T0014 0  0.00    1PHP _ 0
TSCORE T0014 0  0.00    1HUC B 0
TSCORE T0014 0  0.00    1LCT _ 0
TSCORE T0014 0  0.00    1DPB _ 0
TSCORE T0014 0  0.00    1GOF _ 0
TSCORE T0014 0  0.00    2TPR A 0
TSCORE T0014 0  0.00    1AFN A 0
TSCORE T0014 0  0.00    1AOR A 0
TSCORE T0014 0  0.00    1CRL _ 0
TSCORE T0014 0  0.00    2SIL _ 0
TSCORE T0014 0  0.00    1IAE _ 0
TSCORE T0014 0  0.00    1MMO D 0
TSCORE T0014 0  0.00    1NDH _ 0
TSCORE T0014 0  0.00    1TME 1 0
TSCORE T0014 0  0.00    3ADK _ 0
TSCORE T0014 0  0.00    151L _ 0
TSCORE T0014 0  0.00    1SXC A 0
TSCORE T0014 0  0.00    8ATC A 0
TSCORE T0014 0  0.00    1MPP _ 0
TSCORE T0014 0  0.00    1TLF A 0
TSCORE T0014 0  0.00    2ABK _ 0
TSCORE T0014 0  0.00    3PGA 1 0
TSCORE T0014 0  0.00    1NIF _ 0
TSCORE T0014 0  0.00    7API A 0
TSCORE T0014 0  0.00    2KAU C 0
TSCORE T0014 0  0.00    1FC2 D 0
TSCORE T0014 0  0.00    1AOZ A 0
TSCORE T0014 0  0.00    3COX _ 0
TSCORE T0014 0  0.00    1KAP P 0
TSCORE T0014 0  0.00    4ENL _ 0
TSCORE T0014 0  0.00    1TRK A 0
TSCORE T0014 0  0.00    1HUR A 0
TSCORE T0014 0  0.00    1F3G _ 0
TSCORE T0014 0  0.00    3GRS _ 0
TSCORE T0014 0  0.00    1CTN _ 0
TSCORE T0014 0  0.00    1MHL C 0
TSCORE T0014 0  0.00    1ADE A 0
TSCORE T0014 0  0.00    1FBL _ 0
TSCORE T0014 0  0.00    1CYN A 0
TSCORE T0014 0  0.00    2NN9 _ 0
TSCORE T0014 0  0.00    1OMP _ 0
TSCORE T0014 0  0.00    1XIM A 0
TSCORE T0014 0  0.00    1LMW B 0
TSCORE T0014 0  0.00    1AMG _ 0
TSCORE T0014 0  0.00    1CTF _ 0
TSCORE T0014 0  0.00    1PHO _ 0
TSCORE T0014 0  0.00    1HDR _ 0
TSCORE T0014 0  0.00    1ORD A 0
TSCORE T0014 0  0.00    1BGL A 0
TSCORE T0014 0  0.00    2OHX A 0
TSCORE T0014 0  0.00    1IGC L 0
TSCORE T0014 0  0.00    2FB4 H 0
TSCORE T0014 0  0.00    1PCR H 0
TSCORE T0014 0  0.00    8ACN _ 0
TSCORE T0014 0  0.00    1NPK _ 0
TSCORE T0014 0  0.00    1FBI H 0
TSCORE T0014 0  0.00    1LPF A 0
TSCORE T0014 0  0.00    1GLC G 0
TSCORE T0014 0  0.00    1ARS _ 0
TSCORE T0014 0  0.00    1PCA _ 0
TSCORE T0014 0  0.00    1PKY C 0
REMARK ========================================================================
REMARK Alignment of target to 1CTT, chain _
TALIGN T0014 0     1    56   1CTT _ 0     9    64 1.0  1
TALIGN T0014 0    57   146   1CTT _ 0    66   155 1.0  1
TALIGN T0014 0   150   175   1CTT _ 0   156   181 1.0  1
TALIGN T0014 0   176   206   1CTT _ 0   183   213 1.0  1
TALIGN T0014 0   210   252   1CTT _ 0   214   256 1.0  1
REMARK Alignment of target to 2MNR, chain _
TALIGN T0014 0     1    84   2MNR _ 0   105   188 1.0  1
TALIGN T0014 0    89    92   2MNR _ 0   189   192 1.0  1
TALIGN T0014 0    97   140   2MNR _ 0   193   236 1.0  1
TALIGN T0014 0   141   252   2MNR _ 0   239   350 1.0  1
REMARK Alignment of target to 1BNH, chain _
TALIGN T0014 0     1    38   1BNH _ 0    32    69 1.0  1
TALIGN T0014 0    42   233   1BNH _ 0    70   261 1.0  1
TALIGN T0014 0   236   252   1BNH _ 0   262   278 1.0  1
REMARK Alignment of target to 1IVD, chain _
TALIGN T0014 0     1    29   1IVD _ 0   114   142 1.0  1
TALIGN T0014 0    30   178   1IVD _ 0   144   292 1.0  1
TALIGN T0014 0   181   252   1IVD _ 0   293   364 1.0  1
REMARK Alignment of target to 1IRK, chain _
TALIGN T0014 0     1   128   1IRK _ 0  1008  1135 1.0  1
TALIGN T0014 0   129   156   1IRK _ 0  1137  1164 1.0  1
TALIGN T0014 0   157   205   1IRK _ 0  1167  1215 1.0  1
TALIGN T0014 0   206   252   1IRK _ 0  1217  1263 1.0  1
REMARK Alignment of target to 1PPO, chain _
TALIGN T0014 0     9   142   1PPO _ 0     1   134 1.0  1
TALIGN T0014 0   145   215   1PPO _ 0   135   205 1.0  1
TALIGN T0014 0   218   228   1PPO _ 0   206   216 1.0  1
REMARK Alignment of target to 1NIP, chain A
TALIGN T0014 0     1    22   1NIP A 0     5    26 1.0  1
TALIGN T0014 0    23    91   1NIP A 0    31    99 1.0  1
TALIGN T0014 0    92   128   1NIP A 0   103   139 1.0  1
TALIGN T0014 0   129   180   1NIP A 0   141   192 1.0  1
TALIGN T0014 0   181   233   1NIP A 0   194   246 1.0  1
TALIGN T0014 0   236   252   1NIP A 0   247   263 1.0  1
REMARK Alignment of target to 1WHT, chain A
TALIGN T0014 0    10    52   1WHT A 0    -5    38 1.0  1
TALIGN T0014 0    53   174   1WHT A 0    40   158 1.0  1
TALIGN T0014 0   175   252   1WHT A 0   162   239 1.0  1
REMARK Alignment of target to 1FCD, chain A
TALIGN T0014 0     1    13   1FCD A 0   160   172 1.0  1
TALIGN T0014 0    18    87   1FCD A 0   173   242 1.0  1
TALIGN T0014 0    91   125   1FCD A 0   243   277 1.0  1
TALIGN T0014 0   126   158   1FCD A 0   279   311 1.0  1
TALIGN T0014 0   161   250   1FCD A 0   312   401 1.0  1
REMARK Alignment of target to 1LCP, chain A
TALIGN T0014 0    15    81   1LCP A 0     1    67 1.0  1
TALIGN T0014 0    84   124   1LCP A 0    68   108 1.0  1
TALIGN T0014 0   126   174   1LCP A 0   109   157 1.0  1
TALIGN T0014 0   178   252   1LCP A 0   158   232 1.0  1
REMARK =================== End of entry for prediction competition  ===========
REMARK # 15 July 96
REMARK puts -nonewline "Running from "
REMARK puts "[pwd]"
REMARK puts "First calculation on T0014, 252 residues, 3-Dehydroquinase"
REMARK puts "Using all atom tanh force field with residue averaging"
REMARK puts "Searching entire PDB library"
REMARK puts "Small, 3000, ovrlp_scl"
REMARK puts "Penalty for ovrlp_scl is 30 (rather low) and the pnlty_scl"
REMARK puts "is running from 4000 to 7000"
REMARK 
REMARK version
REMARK 
REMARK set OVRLP_SCL_1 2500
REMARK 
REMARK set PNLTY_SCL_2  750
REMARK set OVRLP_SCL_2  250
REMARK # How many structures to subject to Monte Carlo ?
REMARK set NUM_MC 30
REMARK # First mc run
REMARK set MC1_INI 50
REMARK set MC1_FNL  5
REMARK set MC2_INI 50
REMARK set MC2_FNL  0
REMARK 
REMARK set scr_func score_tanh_cxa
REMARK set enrgy_av   1.0
REMARK set do_nrgy_shft 1
REMARK set algn_iter 0
REMARK 
REMARK set mc_max_mv 3
REMARK set mc_steps 10000
REMARK 
REMARK set PDBLIB       /scr1/torda/t14lib
REMARK set PARAM_FILE   /users/torda/c/align/tests/cx_allat.param.gz
REMARK set SECOND_PARAM /users/torda/c/align/tests/cc_allat_p370+0.param.gz
REMARK set SEQ_FILE     ./t14.seq
REMARK 
REMARK 
REMARK set cptn_auth \
REMARK "8076-4866-8089 Thomas Huber, Chris Dyer, Tian-Xiong Lu and Andrew Torda
REMARK 8076-4866-8089 Research School of Chemistry
REMARK 8076-4866-8089 Australian National University
REMARK 8076-4866-8089 Canberra, ACT 0200
REMARK 8076-4866-8089 Australia
REMARK 8076-4866-8089 Thomas.Huber@anu.edu.au, dyer@rsc.anu.edu.au,
REMARK 8076-4866-8089 lu_t@rsc.anu.edu.au, Andrew.Torda@anu.edu.au
REMARK 8076-4866-8089 http://rsc.anu.edu.au/~torda, fax: +61-6-249 0750"
REMARK 
REMARK version
REMARK dump_vars
REMARK 
REMARK set seq [open_str text $SEQ_FILE]
REMARK puts "Sequence info:"
REMARK info_str $seq
REMARK 
REMARK set cptn_trgt "T0014"
REMARK 
REMARK foreach v {4500 6250 8000 } {
REMARK 
REMARK #   Set up the alignment summary
REMARK     set summary [open_str libsrch $seq]
REMARK 
REMARK #   Loop over structures in PDBLIB dir
REMARK     set pnlty_scl $v
REMARK     puts ""
REMARK     puts "Now running with pnlty_scl at $pnlty_scl in non-specific force field"
REMARK     set ovrlp_scl $OVRLP_SCL_1
REMARK     set parm [open_str param $PARAM_FILE]
REMARK     foreach f  [dir_list $PDBLIB] {
REMARK         set coord [open_str coord   $PDBLIB/$f]
REMARK         set algn  [open_str t_align $coord $seq $parm]
REMARK         add_algn $summary $algn
REMARK         close_str $algn
REMARK         close_str $coord
REMARK     }
REMARK     close_str $parm
REMARK     libsrch_sort gap_tmpl $summary
REMARK     libsrch_sort gap_seq  $summary
REMARK     libsrch_sort scr_tot  $summary
REMARK     puts "\nSorted by total score in first, non-specific force field"
REMARK     set nm_prnt_algn 100
REMARK     set verbosity 2
REMARK     print_str $summary
REMARK     flush stdout
REMARK     set verbosity 2
REMARK 
REMARK     set ovrlp_scl $OVRLP_SCL_2
REMARK     set pnlty_scl $PNLTY_SCL_2
REMARK     set parm [open_str param $SECOND_PARAM]
REMARK     puts "Rescore, resort in all-atom force field with"
REMARK     puts "pnlty_scl = $pnlty_scl and ovrlp_scl = $ovrlp_scl"
REMARK     libsrch_rescore $summary $parm
REMARK     libsrch_sort scr_tot $summary
REMARK     set verbosity 1
REMARK     print_str $summary
REMARK     flush stdout
REMARK 
REMARK     set mc_t_ini $MC1_INI
REMARK     set mc_t_fnl $MC1_FNL
REMARK 
REMARK     puts "Begin first MC"
REMARK     libsrch_mc $summary $parm $NUM_MC
REMARK     libsrch_sort scr_tot $summary
REMARK     set nm_prnt_algn $NUM_MC
REMARK     puts "After first MC:"
REMARK     print_str $summary
REMARK     flush stdout
REMARK 
REMARK     set mc_t_ini $MC2_INI
REMARK     set mc_t_fnl $MC2_FNL
REMARK     puts "Begin second MC"
REMARK     libsrch_mc $summary $parm $NUM_MC
REMARK     libsrch_sort scr_tot $summary
REMARK     set nm_prnt_algn $NUM_MC
REMARK     puts "After second MC:"
REMARK     set verbosity 3
REMARK     print_str $summary
REMARK     flush stdout
REMARK     set nm_prnt_algn 10
REMARK     cptn_prnt $summary cptn_out.$v.$pnlty_scl.$ovrlp_scl
REMARK 
REMARK     close_str $parm
REMARK     close_str $summary
REMARK }
REMARK 
REMARK close_str $seq
REMARK =====  Version identifier strings ====================================
REMARK      $Id: aa_conv.c,v 1.15 1996/06/23 01:04:03 torda Exp $
REMARK      $Id: commands.c,v 1.23 1996/07/12 04:05:39 torda Exp $
REMARK      $Id: cc_allat_x.c,v 1.1 1996/07/09 02:27:21 torda Exp $
REMARK      $Id: cptnprnt.c,v 1.6 1996/07/13 10:02:59 torda Exp $
REMARK      $Id: e_malloc.c,v 1.5 1996/07/05 01:40:16 torda Exp $
REMARK      $Id: getcoord.c,v 1.29 1996/07/16 04:27:22 torda Exp $
REMARK      $Id: main.c,v 1.4 1996/03/19 23:08:39 torda Exp $
REMARK      $Id: mgc_num.c,v 1.1 1996/06/05 06:21:47 torda Exp $
REMARK      $Id: misc.c,v 1.4 1996/07/05 01:47:33 torda Exp $
REMARK      $Id: pdbout.c,v 1.16 1996/07/13 09:58:35 torda Exp $
REMARK      $Id: reg_str.c,v 1.5 1996/05/15 11:46:16 torda Exp $
REMARK      $Id: s_s_alin.c,v 1.47 1996/07/12 04:12:54 torda Exp $
REMARK      $Id: s_cmd.c,v 1.24 1996/07/12 03:59:38 torda Exp $
REMARK      $Id: s_obj.c,v 1.70 1996/07/18 08:59:12 torda Exp $
REMARK      $Id: scorefct.c,v 1.8 1996/07/05 02:09:37 torda Exp $
REMARK      $Id: str_up.c,v 1.3 1996/07/05 04:55:35 torda Exp $
REMARK      $Id: tcl_main.c,v 1.2 1996/03/19 22:30:25 torda Exp $
REMARK      $Id: vars.c,v 1.29 1996/07/12 04:15:16 torda Exp $
REMARK      $Id: vrsn_cmd.c,v 1.1 1996/03/11 11:46:59 torda Exp $
REMARK      $Id: zfopen.c,v 1.5 1996/07/12 03:58:03 torda Exp $
REMARK      $Id: myrand.c,v 1.9 1996/07/09 02:26:02 torda Exp $
REMARK      $Revision: 1.6 $

