Subject: Re: Re: "Array too small. Increase MBNDPF"
From: Bozidar Yerkovich <>
Date: Thu, 15 Aug 2002 09:05:04 -0400 (EDT)
Cc: "" <>
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
> >> ---------------------------------
> >>
> >>
> >
> >.
>
> = = = = = = = = = = = = = = = = = = = =
>
>
>
>