[Date Prev][Date Next][Thread Prev][Thread Next][Date Index][Thread Index]
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
> >> ---------------------------------
> >>
> >>
> >
> >.
>
> = = = = = = = = = = = = = = = = = = = =
>
>
>
>