Subject: CCL:GAMESS/TINKER - PROBLEM WITH DLC COORDINATES

From: Dr Seth OLSEN <s.olsen1<<at>>uq.edu.au>
Date: Tue, 11 Jan 2005 11:49:37 +1000

Dear Colleagues,

My input for GAMESS/TINKER is a 98 atom peptide containing a modified tripeptide.  The modified sequence is to be included in the QM/MM region of a GAMESS/TINKER optimization.  I have included NZVAR=288 in the $CNTRL and my $ZMAT deck includes the directives DLC=.T. and AUTO=.T.  However, the job fails with the error:

 ERROR: CURRENT QMMM IMPLEMENTATION REQUIRES DLC COORDINATES (SEE $ZMAT)

The molecule does not contain any I have been reading the manual and experimenting with the input, as I anticipate that somehow I have failed to enter the combination of NZVAR and the $ZMAT deck in the correct manner.  If one of you has time (or the error is sufficiently transparent to you), could you lend a hint?  (Thanks to Brian Salter-Duke for his earlier help)  My input deck follows:

--$CNTRL EXETYP=CHECK $END
 $CNTRL SCFTYP=RHF RUNTYP=optimize MULT=1 EXETYP=RUN COORD=TINKER ICHARG=-1
 NZVAR=288  $END
 $BASIS GBASIS=sto NGAUSS=3 $END
 $ZMAT  DLC=.T. AUTO=.T. $END
 $TINXYZ
 98 molden generated tinker .xyz (mm3 param.)
    1  C     1.124320   -1.779122   -5.825405  20009     2    6   74
    2  C     1.390048   -0.427314   -6.208361  20002     1    3    7
    3  C     1.385198   -0.108612   -7.595450  20002     2    4   73
    4  C     1.123963   -1.102110   -8.579234  20009     3    5   75
    5  C     0.863466   -2.433252   -8.176489  20002     4    6   25
    6  C     0.861515   -2.784286   -6.799471  20001     1    5   76
    7  C     1.674909    0.638310   -5.162475  20002     2    8   72
    8  C     2.409374    0.791493   -3.995053  20002     7    9   12
    9  N     2.559668    2.032807   -3.447687  20002     8   10
   10  C     3.282523    1.901011   -2.323878  20002     9   11   20
   11  N     3.643847    0.521383   -2.090885  20002    10   12   14
   12  C     3.091461   -0.221385   -3.163879  20002     8   11   13
   13  O     3.191780   -1.446907   -3.324064  20006    12
   14  C     4.467595   -0.119208   -0.937780  20006    11   15   71   98
   15  C     3.997365   -0.216337    0.142884  20002    14   16   26
   16  N     2.735860    0.221655    0.296373  20002    15   17   79
   17  C     2.090153    0.180804    1.609199  20007    16   18   43   80
   18  C     1.984037    1.604563    2.154295  20001    17   19   81   82
   19  O     1.383838    1.633183    3.440250  20009    18   94
   20  C     3.599556    3.065571   -1.539910  20002    10   21   27
   21  C     2.833227    4.364367   -1.768142  20001    20   22   69   97
   22  C     2.237452    5.011107   -0.507704  20009    21   23   70   96
   23  C     1.865011    6.456834   -0.576498  20002    22   24   42
   24  N     1.369227    7.017305    0.563700  20001    23   77   78
   25  O     0.608228   -3.385039   -9.132900  20008     5
   26  O     4.713328   -0.722069    1.136396  20002    15
   27  N     4.553110    3.025071   -0.702565  20002    20   28
   28  C     5.701151    3.603317   -0.463185  20002    27   29   30
   29  O     5.682664    3.786086    0.754127  20007    28
   30  C     6.872778    4.044189   -1.309536  20009    28   31   33   65
   31  C     6.693646    5.514413   -1.682226  20009    30   32   66   67
   32  S     8.034581    6.170017   -2.673643  20001    31   68
   33  N     6.941820    3.234319   -2.521573  20002    30   34   64
   34  C     7.659299    2.117949   -2.590469  20007    33   35   36
   35  O     8.294530    1.667797   -1.632398  20001    34
   36  C     7.647413    1.395339   -3.943763  20007    34   37   41   57
   37  C     9.039836    1.531623   -4.574300  20007    36   38   58   59
   38  C     9.117898    1.293351   -6.088438  20001    37   39   60   61
   39  C     8.287458    0.117998   -6.555634  20015    38   40   49
   40  N     7.808837    0.192389   -7.798742  20007    39   62   63
   41  N     6.608656    1.941550   -4.831019  20001    36   55   56
   42  O     2.007205    7.101497   -1.621382  20001    23
   43  C     0.705437   -0.446003    1.468128  20002    17   44   48
   44  N     0.713449   -1.740105    1.180043  20007    43   45   83
   45  C    -0.492284   -2.514812    0.933964  20009    44   46   50   84
   46  C    -0.116283   -3.969867    0.558810  20009    45   47   53   85
   47  C    -1.198101   -4.572065   -0.326708  20001    46   88   89   90
   48  O    -0.328762    0.210937    1.636028  20002    43
   49  O     8.083457   -0.852453   -5.819203  20000    39
   50  C    -1.579338   -2.549762    2.016295  20001    45   51   52
   51  O    -2.609380   -3.198814    1.831173  20001    50
   52  O    -1.399392   -1.844428    3.212172  20001    50   95
   53  C     1.222349   -3.993315   -0.198492  20001    46   54   86   87
   54  C     1.241007   -3.165103   -1.480834  20007    53   91   92   93
   55  H     5.966926    1.187291   -5.114175  20005    41
   56  H     6.080846    2.672126   -4.332446  20005    41
   57  H     7.408684    0.332164   -3.793209  20005    36
   58  H     9.401532    2.551114   -4.374760  20005    37
   59  H     9.651659    0.739995   -4.117140  20005    37
   60  H     8.761669    2.198208   -6.602574  20005    38
   61  H    10.167048    1.064966   -6.327444  20005    38
   62  H     8.005370    0.989685   -8.360630  20005    40
   63  H     7.255347   -0.549426   -8.163961  20005    40
   64  H     6.433645    3.528482   -3.324850  20005    33
   65  H     7.806053    3.916187   -0.741546  20005    30
   66  H     5.757689    5.617753   -2.250824  20005    31
   67  H     6.676863    6.086243   -0.742688  20005    31
   68  H     9.178972    6.216096   -1.921880  20005    32
   69  H     2.298758    4.556665   -2.664884  20005    21
   70  H     2.362693    4.566932    0.448230  20005    22
   71  H     4.776843   -1.132348   -1.006291  20005    14
   72  H     1.129903    1.501971   -5.571202  20005     7
   73  H     1.580139    0.888958   -7.901449  20005     3
   74  H     1.122910   -2.038240   -4.796018  20005     1
   75  H     1.124432   -0.846417   -9.609479  20005     4
   76  H     0.666471   -3.783937   -6.500411  20005     6
   77  H     1.271089    6.466796    1.386702  20005    24
   78  H     1.105651    7.976719    0.572554  20005    24
   79  H     2.237332    0.576270   -0.488320  20005    16
   80  H     2.682543   -0.426595    2.309297  20005    17
   81  H     2.993678    2.035748    2.222904  20005    18
   82  H     1.351204    2.187001    1.468519  20005    18
   83  H     1.591181   -2.206000    1.129534  20005    44
   84  H    -0.964629   -1.956780    0.112081  20005    45
   85  H    -0.023795   -4.557661    1.483984  20005    46
   86  H     2.002968   -3.605036    0.472235  20005    53
   87  H     1.392521   -5.037676   -0.499077  20005    53
   88  H    -1.677768   -5.411062    0.198654  20005    47
   89  H    -1.951985   -3.804978   -0.557442  20005    47
   90  H    -0.746205   -4.935411   -1.261464  20005    47
   91  H     0.738289   -3.722234   -2.285123  20005    54
   92  H     0.715894   -2.213683   -1.310363  20005    54
   93  H     2.282527   -2.962591   -1.771050  20005    54
   94  H     1.334403    2.531030    3.746726  20000    19
   95  H    -2.157866   -1.968974    3.770477  20000    52
   96  H     1.160097    5.003378   -0.349065      0    22
   97  H     3.355150    5.319202   -1.725625      0    21
   98  H     5.354551    0.511008   -0.892414      0    14
 $END
 $LINK
IMOMM=.T.
IQMATM(1)=20,37,19,18,5,1,2,3,4,15,71,98,14,6,72,7,12,74,11,76,10,13,9,75,8,73
 $END
 $TINKEY
parameters /home/seth/gamess/tinker/params/mm3
 $END

Cheers,

Seth

ccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccms

Dr Seth Olsen, PhD
Postdoctoral Fellow, Computational Systems Biology Group
Centre for Computational Molecular Science
Chemistry Building,
The University of Queensland
Qld 4072, Brisbane, Australia

tel (617) 33653732
fax (617) 33654623
email: s.olsen1<<at>>uq.edu.au
Web: www.ccms.uq.edu.au 

ccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccms

----- Original Message -----
From: Brian Salter-Duke <b_duke<<at>>octa4.net.au>
Date: Tuesday, January 11, 2005 9:07 am
Subject: Re: CCL:GAMESS/TINKER IMOMM - $DATA needed?

> On Mon, Jan 10, 2005 at 03:25:17PM +1000, Dr Seth OLSEN wrote:
> > 
> > Dear Collegues,
> > 
> > I'm training myself on GAMESS/TINKER.  The cyclopentene test jobs 
> that are 
> > found in the documentation by Cheol Ho Choi run fine on my 
> installation, so 
> > I have tried to work up my own input for a short peptide with a 
> modified AA 
> > in the quantum region.  When I attempt to run it, GAMESS 
> terminates an error 
> > saying that no $DATA group was found.  However, the documentation 
> states that 
> > if all the coordinates are to be given in the $TINKEY field for 
> an IMOMM job 
> > than no $DATA group should be necessary.  Moreover, the 
> cyclopentene IMOMM 
> > job with the commented-out $DATA field works fine.  Can anyone 
> tell me what 
> > is going wrong.  My input deck follows:
> 
> Seth,
> 
> Is this really your input deck? There must be a space before every
> control work and before $END. Your deck is all comment - no data at 
> all.
> Cheers, Brian.
> 
> > $CNTRL SCFTYP=RHF RUNTYP=optimize MULT=1 EXETYP=RUN COORD=TINKER 
> ICHARGE=-1
> > NZVAR=288 $END
> > $BASIS GBASIS=sto NGAUSS=3 $END
> > $ZMAT DLC=.T. AUTO=.T. $END
> > $TINXYZ
> >  98 molden generated tinker .xyz (mm3 param.)
> >     1  N     2.559668    2.032808   -3.447687      9     2    5
> >     2  C     2.409374    0.791493   -3.995053      2     1    3   
> 6
> >     3  C     3.091461   -0.221384   -3.163879      2     2    4   14
> >     4  N     3.643847    0.521384   -2.090885      9     3    5   15
> >     5  C     3.282523    1.901012   -2.323878      2     1    4   18
> >     6  C     1.674909    0.638310   -5.162475      1     2    7   72
> >     7  C     1.390048   -0.427314   -6.208361      2     6    8   12
> >     8  C     1.385198   -0.108612   -7.595450      2     7    9   73
> >     9  C     1.123963   -1.102110   -8.579234      2     8   10   75
> >    10  C     0.863466   -2.433252   -8.176489      2     9   11   13
> >    11  C     0.861515   -2.784286   -6.799471      2    10   12   76
> >    12  C     1.124320   -1.779122   -5.825405      2     7   11   74
> >    13  O     0.608228   -3.385039   -9.132900      6    10
> >    14  O     3.191780   -1.446907   -3.324064      6     3
> >    15  C     4.467595   -0.119207   -0.937780      2     4   16   
> 71   98
> >    16  C     3.997365   -0.216336    0.142884      2    15   17   31
> >    17  O     4.713328   -0.722068    1.136396      7    16
> >    18  C     3.599556    3.065572   -1.539910      1     5   19   26
> >    19  N     4.553110    3.025072   -0.702565      9    18   20
> >    20  C     5.684243    3.302363   -0.108162      2    19   21   37
> >    21  C     7.092847    3.591389   -0.572584      1    20   22   
> 38   65
> >    22  N     7.327498    2.960719   -1.867530      9    21   23   64
> >    23  C     7.830224    1.735879   -1.980832      2    22   24   40
> >    24  C     8.039690    1.226535   -3.412755      1    23   25   
> 41   57
> >    25  N     7.377170    2.101644   -4.392468      8    24   55   56
> >    26  C     2.833227    4.364368   -1.768142      2    18   27   
> 69   97
> >    27  C     2.237451    5.011108   -0.507705      2    26   28   
> 70   96
> >    28  C     1.865011    6.456835   -0.576499      2    27   29   30
> >    29  O     2.007205    7.101498   -1.621383      7    28
> >    30  N     1.369226    7.017306    0.563699      9    28   77   78
> >    31  N     2.735860    0.221656    0.296373      9    16   32   79
> >    32  C     2.090153    0.180805    1.609199      1    31   33   
> 35   80
> >    33  C     0.705437   -0.446002    1.468128      2    32   34   46
> >    34  O    -0.328762    0.210937    1.636028      7    33
> >    35  C     1.984037    1.604564    2.154295      1    32   36   
> 81   82
> >    36  O     1.383837    1.633184    3.440250      7    35   94
> >    37  O     5.385773    3.315266    1.086135      7    20
> >    38  C     7.277566    5.102506   -0.694850      1    21   39   
> 66   67
> >    39  S     8.922188    5.582399   -1.219971     15    38   68
> >    40  O     8.108043    1.031231   -1.005976      7    23
> >    41  C     9.548903    1.143626   -3.678073      1    24   42   
> 58   59
> >    42  C     9.970547    1.105082   -5.153271      1    41   43   
> 60   61
> >    43  C     9.094567    0.213307   -6.005771      2    42   44   45
> >    44  O     8.540316   -0.781940   -5.528265      7    43
> >    45  N     8.972657    0.560148   -7.288256      9    43   62   63
> >    46  N     0.713449   -1.740104    1.180043      9    33   47   83
> >    47  C    -0.492284   -2.514811    0.933964      1    46   48   
> 50   84
> >    48  C    -1.579338   -2.549761    2.016295      2    47   49   54
> >    49  O    -1.399392   -1.844427    3.212172      0    48   95
> >    50  C    -0.116283   -3.969867    0.558810      1    47   51   
> 53   85
> >    51  C     1.222349   -3.993314   -0.198492      1    50   52   
> 86   87
> >    52  C     1.241007   -3.165103   -1.480834      1    51   91   
> 92   93
> >    53  C    -1.198101   -4.572065   -0.326708      1    50   88   
> 89   90
> >    54  O    -2.609380   -3.198813    1.831173      7    48
> >    55  H     6.707356    1.550632   -4.948018      5    25
> >    56  H     6.876161    2.853334   -3.897643      5    25
> >    57  H     7.586799    0.229924   -3.520723      5    24
> >    58  H    10.020885    2.023145   -3.215816      5    41
> >    59  H     9.873152    0.183037   -3.251307      5    41
> >    60  H     9.923758    2.127612   -5.556067      5    42
> >    61  H    10.988634    0.690100   -5.189157      5    42
> >    62  H     9.444407    1.365605   -7.632806      5    45
> >    63  H     8.409984    0.013364   -7.900181      5    45
> >    64  H     7.103100    3.465759   -2.694940      5    22
> >    65  H     7.810952    3.187315    0.156146      5    21
> >    66  H     6.552723    5.483409   -1.429367      5    38
> >    67  H     7.120716    5.529345    0.306753      5    38
> >    68  H     9.824291    5.275534   -0.235621      5    39
> >    69  H     2.298758    4.556666   -2.664884      5    26
> >    70  H     2.362692    4.566933    0.448229      5    27
> >    71  H     4.776843   -1.132347   -1.006291      5    15
> >    72  H     1.129903    1.501971   -5.571202      5     6
> >    73  H     1.580139    0.888958   -7.901449      5     8
> >    74  H     1.122910   -2.038240   -4.796018      5    12
> >    75  H     1.124432   -0.846417   -9.609479      5     9
> >    76  H     0.666471   -3.783937   -6.500411      5    11
> >    77  H     1.271088    6.466797    1.386701      5    30
> >    78  H     1.105651    7.976720    0.572553      5    30
> >    79  H     2.237332    0.576271   -0.488320      5    31
> >    80  H     2.682543   -0.426594    2.309297      5    32
> >    81  H     2.993677    2.035749    2.222904      5    35
> >    82  H     1.351203    2.187002    1.468519      5    35
> >    83  H     1.591181   -2.205999    1.129534      5    46
> >    84  H    -0.964629   -1.956780    0.112081      5    47
> >    85  H    -0.023795   -4.557660    1.483984      5    50
> >    86  H     2.002968   -3.605035    0.472235      5    51
> >    87  H     1.392521   -5.037675   -0.499077      5    51
> >    88  H    -1.677768   -5.411062    0.198654      5    53
> >    89  H    -1.951985   -3.804978   -0.557442      5    53
> >    90  H    -0.746205   -4.935411   -1.261464      5    53
> >    91  H     0.738289   -3.722234   -2.285123      5    52
> >    92  H     0.715894   -2.213683   -1.310363      5    52
> >    93  H     2.282527   -2.962591   -1.771050      5    52
> >    94  H     1.334402    2.531031    3.746726      0    36
> >    95  H    -2.157866   -1.968973    3.770477      0    49
> >    96  H     1.160096    5.003379   -0.349066  20000    27
> >    97  H     3.355150    5.319203   -1.725626  20000    26
> >    98  H     5.354551    0.511009   -0.892414  20000    15
> > $END
> > $LINK
> > IMOMM=.T.
> > 
> IQMATM=20,37,19,18,5,1,2,3,4,15,71,98,14,6,72,7,12,74,11,76,10,13,9,75,8,73> LINKGE=15,16, 20,21, 18,26
> > $END
> > $TINKEY
> > parameters /home/seth/gamess/tinker/params/mm3
> > $END
> > 
> > 
> > Cheers,
> > 
> > Seth Olsen
> > 
> > ccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccms
> > 
> > Dr Seth Olsen, PhD
> > Postdoctoral Fellow, Computational Systems Biology Group
> > Centre for Computational Molecular Science
> > Chemistry Building,
> > The University of Queensland
> > Qld 4072, Brisbane, Australia
> > 
> > tel (617) 33653732
> > fax (617) 33654623
> > email: s.olsen1<<at>>uq.edu.au
> > Web: www.ccms.uq.edu.au 
> > 
> > ccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccms
> > 
> > 
> > 
> > 
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> > 
> 
> -- 
>            Brian Salter-Duke (Brian Duke) b_duke<<at>>octa4.net.au  
>         Post: 626 Melbourne Rd, Spotswood, VIC, 3015, Australia
>      Phone 03-92992847. http://members.iinet.net.au/~linden1/brian/
>