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 >> --------------------------------- >> >> > >.
= = = = = = = = = = = = = = = = = = = =
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 > >> --------------------------------- > >> > >> > > > >. > > = = = = = = = = = = = = = = = = = = = = > > > >
Hi group,
I am looking for this __sidehchain.top script (for modeling point mutation) that was supposed to be in the /bin/_*.top files.
I just wonder if this script was really left out in v6.2 of Modeler. (Couldn't find it in my installed version...)
Anyone out there with a previous Modeler version who might be able to post the __sidehchain.top script?
Thanks in advance,
jonathan
========================= Structural Chemistry Medical Biochemistry Dept. Göteborg University SWEDEN tel#: +46(0)73 718 88 37 =========================
It was left out on purpose. I can send you the script but un-officially ;-)
Best, Bozidar Yerkovich
On Fri, 16 Aug 2002, Jonathan Esguerra wrote:
> > Hi group, > > I am looking for this __sidehchain.top script (for modeling point > mutation) that was supposed to be in the /bin/_*.top files. > > I just wonder if this script was really left out in v6.2 of Modeler. > (Couldn't find it in my installed version...) > > Anyone out there with a previous Modeler version who > might be able to post the __sidehchain.top script? > > Thanks in advance, > > jonathan > > > ========================= > Structural Chemistry > Medical Biochemistry Dept. > Göteborg University > SWEDEN > tel#: +46(0)73 718 88 37 > ========================= > >
participants (3)
-
Bozidar Yerkovich -
Jonathan Esguerra -
Kong Lesheng