Subject: Re: Re: "Array too small. Increase MBNDPF"
From: Kong Lesheng <>
Date: Thu, 15 Aug 2002 19:12:6 +0800
Cc: "" <>
Organization: NUS
Reply-to:
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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