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



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
>> ---------------------------------
>> 
>> 
>
>.

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