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Re: Re: "Array too small. Increase MBNDPF"



Great, I'll try to put it on the web, for others to use, if that's OK?

Best,
Bozidar

On Thu, 15 Aug 2002, Kong Lesheng wrote:

> Dear Dr. Bozidar Yerkovich,
> Thank you very much for your kind help!
> I have solved this problem! :-)
> The error message is due to problems of my topology files format.
> I have modified the RTF file, and now I can generate models including HYP!
> 
> My topology files for HYP as follows:
> RESI HYP	0.00000
> GROUP                   !       HD1 HD2
> ATOM N    N    -0.29    !     |   \ / 
> ATOM CA   CP1   0.02    !     N---CD   HG
> ATOM HA   HB    0.09    !     |     \  /
> ATOM CD   CP3   0.18    !     |      CG
> ATOM HD1  HB    0.00    !     |     /  \
> ATOM HD2  HB    0.00    !  HA-CA--CB   OG2--HG2
> GROUP                   !     |   / \
> ATOM CB   CP2  -0.18    !     | HB1 HB2
> ATOM HB1  HA    0.09    !   O=C
> ATOM HB2  HA    0.09    !     |
> GROUP
> ATOM CG   CT1   0.14
> ATOM HG   HA    0.09
> ATOM OG2  OH1  -0.66
> ATOM HG2  H     0.43
> GROUP
> ATOM C    CC    0.53 
> ATOM O    O    -0.53
> BOND O  C   C   CA  C   +N   
> BOND N  CA  CA  CB  CB  CG  CG  CD  N   CD  CG  OG2   
> BOND HA CA  HG  CG  HG2 OG2 HD1 CD  HD2 CD  HB1 CB  HB2 CB
> IMPR N -C CA CD   
> IMPR C CA +N O   
> IMPR CA N C CB    
> DONOR HG2 OG2
> ACCEPTOR O C 
> IC CD   N    CA   CB    1.4468  114.9587  -11.2918  101.8808  1.5360
> IC CD   N    CA   HA    1.4468  114.9587 -129.2290  110.5162  1.0924
> IC CD   N    CA   C     1.4468  114.9587  109.5875  111.6376  1.5380
> IC HA   CA   N    +C    1.0924  110.5162   50.0429  122.5076  1.3162
> IC CD   +C   *N   CA    1.4468  122.5296 -179.2170  122.5076  1.4550
> IC CA   N    CD   CG    1.4550  114.9587  -11.8599  102.4794  1.5305
> IC CA   N    CD   HD1   1.4550  114.9587 -131.8901  111.1069  1.0924
> IC CA   N    CD   HD2   1.4550  114.9587  106.0401  109.5406  1.0925
> IC N    CA   CB   CG    1.4550  101.8808   29.6080  103.6605  1.5362
> IC N    CA   CB   HB1   1.4550  101.8808  152.0681  112.9350  1.0925
> IC N    CA   CB   HB2   1.4550  101.8808  -86.5729  108.9663  1.0930
> IC N    CA   C    O     1.4550  111.6376  149.4002  120.4223  1.2316
> IC N    CA   C    N     1.4550  111.6376  -31.0428  120.0469  1.3161
> IC N    CA   *C   O     1.3161  120.0469 -179.5571  120.4223  1.2316
> IC CA   CB   CG   OG2   1.5360  103.6605 -158.7449  112.5784  1.4300
> IC CA   CB   CG   HG    1.5360  103.6605   79.0616  109.5554  1.0926
> IC CD   CG   OG2  HG2   1.5305  112.2089   31.3937  109.5000  1.0300
> IC N    CD   CG   CB    1.4468  102.4794   29.9288  103.3139  1.5362
> PATCHING FIRS PROP
> 
> 
> Thanks a lot!
> With best regards,
> Kong Lesheng
> ---------------------------------
> BioInformatics Center
> National University of Singapore
> 10 Kent Ridge Cresent
> Singapore119260
> Tel: (65)6874 4459
> Fax: (65)6778 2466
> ---------------------------------
> 
> ======= 2002-08-12 You write==============
> 
> >I'll have to take a closer look at this. I'll let you know...
> >Best,
> >Bozidar
> >
> >
> >On Mon, 12 Aug 2002, Kong Lesheng wrote:
> >
> >> Dear Dr. Bozidar Yerkovich,
> >> I have added topology of HYP into top.lib, and modified restyp.lib(using "o" as residue code for HYP).
> >> But when I did modelling, it reported the following errors and warnings.
> >> addprm__223E> Array too small. Increase  MBNDPF
> >> recover____E> ERROR_STATUS >= STOP_ON_ERROR:        1       1
> >> getf_______W> RTF restraint not found in the atoms list:
> >> getf_______W> RTF restraint not found in the atoms list:
> >> getf_______W> RTF restraint not found in the atoms list:
> >> iatmcls_286W> MODEL atom not classified:  ALA:OT1  ALA
> >> iatmcls_286W> MODEL atom not classified:  ALA:OT2  ALA
> >> r_stere_607W> Cannot find params in params file:
> >> addprm__440W> Adding params (mean,force,period):        1.5431      300.0000        1
> >> r_stere_607W> Cannot find params in params file:
> >> addprm__440W> Adding params (mean,force,period):        3.0698      300.0000        1
> >> r_stere_607W> Cannot find params in params file:
> >> addprm__440W> Adding params (mean,force,period):        1.0924      300.0000        1
> >> r_stere_607W> Cannot find params in params file:
> >> addprm__440W> Adding params (mean,force,period):        3.8828      300.0000        1
> >> r_stere_607W> Cannot find params in params file:
> >> addprm__440W> Adding params (mean,force,period):       66.6866       60.0000        1
> >> r_stere_607W> Cannot find params in params file:
> >> addprm__440W> Adding params (mean,force,period):      111.1069       60.0000        1
> >> .......
> >> 
> >> How could I fix these problem?
> >> I attach an uuencoded compressed tar archive of all input and output files.
> >> Thank you very much!
> >> With best regards,
> >> Kong Lesheng
> >> 
> >> ---------------------------------
> >> BioInformatics Center
> >> National University of Singapore
> >> 10 Kent Ridge Cresent
> >> Singapore119260
> >> Tel: (65)6874 4459
> >> Fax: (65)6778 2466
> >> ---------------------------------
> >> 
> >> 
> >
> >.
> 
> = = = = = = = = = = = = = = = = = = = =
> 			
> 
>                    
>