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 > >> --------------------------------- > >> > >> > > > >. > > = = = = = = = = = = = = = = = = = = = = > > > >