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-- Shahid. On Mon, Nov 30, 2009 at 8:15 PM, FyD <fyd.q4md-forcefieldtools.org> wrote: > Dear Shahid, > > LEaP is unstable if you have errors in a file format. > You modified the mol2 file format in FAD.mol2: > I would first check if the mol2 file format you use is correct > > A google search of "Tripos mol2 file format" provides: > > http://www.tripos.com/index.php?family=modules,SimplePage,,,&page=sup_mol2&s=0 > . > > An example of simple Tripos mol2 file format can be found for DMSO in the > W-1 R.E.DD.B. project: > http://q4md-forcefieldtools.org/REDDB/projects/W-1/tripos1.mol2 > For instance in the .<TRIPOS>MOLECULE section: > 10 9 1 > means 10 atoms, 9 bonds & 1 residue... > > See comments below as well. > > regards, Francois > > > > I used the following paramters which seems not working: >> >> N*-CA 448.0 1.365 JCC,7,(1986),230; CYT,THY,URA >> CA-C -O 70.0 120.00 >> NC-C-NA 70.0 121.50 >> NC-CA-N* 70.0 121.50 >> NC-CA-CA 70.0 121.50 >> N*-CA-CA 70.0 121.50 >> CA-NC-CA 70.0 121.50 >> CA-N*-CA 70.0 121.50 >> C-CA-NC 70.0 121.50 >> CT-N*-CA 70.0 117.60 >> NA-C-CA 70.0 125.20 >> >> and for >> >> ** No torsion terms for CA-CA-N*-CA >> ** No torsion terms for CA-N*-CA-CA >> ** No torsion terms for CA-N*-CA-CA >> ** No torsion terms for NC-CA-N*-CA >> ** No torsion terms for CT-N*-CA-CA >> ** No torsion terms for CT-N*-CA-NC >> ** No torsion terms for CT-N*-CA-CA >> ** No torsion terms for CT-N*-CA-CA >> > > You need to follow a format for the frcmod file loaded in LEaP: > See $AMBERHOME/dat/leap/parm/frcmod.parmbsc0: this file contains all the > sections possible > > > used the parameters >> >> X -N*-CA-X 4 14.50 180.0 2. >> CT-N*-CA-CA 1.0 180. 2. >> > > Here, to check you could edit the FF atom types of the DC, DA and DT > residues available in the Amber force field topology database. > > > then tleap went find and got no complaints >> but at the end converting topology to pdb by ambpdb was not working. >> >> forrtl: severe (174): SIGSEGV, segmentation fault occurred >> Image PC Routine Line >> Source >> ambpdb 0804FBA4 Unknown Unknown Unknown >> ambpdb 0804A1C5 Unknown Unknown Unknown >> ambpdb 08048222 Unknown Unknown Unknown >> ambpdb 080B15A2 Unknown Unknown Unknown >> ambpdb 08048101 Unknown Unknown Unknown >> >> >> I guess I used the wrong parameters. >> > > If a FF parameter has an inappropriate value, LEaP does not crash. > > > I also tried to use FAD params from >> http://www.pharmacy.manchester.ac.uk/bryce/amber >> but also doesn't work in my case. >> >> Best regards, >> >> -- >> Shahid. >> >> >> On Mon, Nov 30, 2009 at 2:02 PM, FyD <fyd.q4md-forcefieldtools.org> >> wrote: >> >> Dear Shahid, >>> >>> Some FF parameters are missing... >>> >>> You need to have a frcmod file for the listed missing force field >>> parameters. >>> >>> >>> Could not find bond parameter for: N* - CA >>> >>>> >>>> >>> You could use/adapt CM-N* for CA-N*, for instance >>> >>> >>> Could not find angle parameter: NC - CA - CA >>> >>>> >>>> >>> Similar idea with NC-CA-CM & NC-CA-CA for instance. >>> >>> For all missing FF parameters, you should find a FF parameter available >>> in >>> $AMBERHOME/dat/leap/parm/parm99.dat you could adapt... >>> >>> regards, Francois >>> >>> >>> >>> I have problems while working with a protein which contain FAD. >>> >>>> Here is what I get: >>>> bash-3.2$ ~/amber/amber10/exe/tleap -f leaprc.ff99SB >>>> -I: Adding /home/shahid/amber/amber10/dat/leap/prep to search path. >>>> -I: Adding /home/shahid/amber/amber10/dat/leap/lib to search path. >>>> -I: Adding /home/shahid/amber/amber10/dat/leap/parm to search path. >>>> -I: Adding /home/shahid/amber/amber10/dat/leap/cmd to search path. >>>> -f: Source leaprc.ff99SB. >>>> >>>> Welcome to LEaP! >>>> (no leaprc in search path) >>>> Sourcing: /home/shahid/amber/amber10/dat/leap/cmd/leaprc.ff99SB >>>> Log file: ./leap.log >>>> Loading parameters: /home/shahid/amber/amber10/dat/leap/parm/parm99.dat >>>> Reading title: >>>> PARM99 for DNA,RNA,AA, organic molecules, TIP3P wat. Polariz.& LP >>>> incl.02/04/99 >>>> Loading parameters: >>>> /home/shahid/amber/amber10/dat/leap/parm/frcmod.ff99SB >>>> Reading force field modification type file (frcmod) >>>> Reading title: >>>> Modification/update of parm99.dat (Hornak & Simmerling) >>>> Loading library: >>>> /home/shahid/amber/amber10/dat/leap/lib/all_nucleic94.lib >>>> Loading library: /home/shahid/amber/amber10/dat/leap/lib/all_amino94.lib >>>> Loading library: >>>> /home/shahid/amber/amber10/dat/leap/lib/all_aminoct94.lib >>>> Loading library: >>>> /home/shahid/amber/amber10/dat/leap/lib/all_aminont94.lib >>>> Loading library: /home/shahid/amber/amber10/dat/leap/lib/ions94.lib >>>> Loading library: /home/shahid/amber/amber10/dat/leap/lib/solvents.lib >>>> >>>> FAD=loadmol2 FAD.mol2 >>>> >>>>> >>>>> Loading Mol2 file: /home/shahid/amber/amber10/dat/leap/cmd/FAD.mol2 >>>> Reading MOLECULE named FAD >>>> >>>> myfad=loadpdb testfad.pdb >>>>> >>>>> Loading PDB file: ./testfad.pdb >>>> total atoms in file: 53 >>>> Leap added 31 missing atoms according to residue templates: >>>> 31 H / lone pairs >>>> >>>> check myfad >>>>> >>>>> Checking 'myfad'.... >>>> WARNING: The unperturbed charge of the unit: -2.000000 is not zero. >>>> Checking parameters for unit 'myfad'. >>>> Checking for bond parameters. >>>> Could not find bond parameter for: N* - CA >>>> Could not find bond parameter for: N* - CA >>>> Checking for angle parameters. >>>> Could not find angle parameter: NC - CA - CA >>>> Could not find angle parameter: NC - CA - CA >>>> Could not find angle parameter: CA - NC - CA >>>> Could not find angle parameter: CA - CA - NC >>>> Could not find angle parameter: CA - N* - CA >>>> Could not find angle parameter: N* - CA - CA >>>> Could not find angle parameter: N* - CA - CA >>>> Could not find angle parameter: N* - CA - CA >>>> Could not find angle parameter: O - C - CA >>>> Could not find angle parameter: C - CA - NC >>>> Could not find angle parameter: NA - C - CA >>>> Could not find angle parameter: NC - C - NA >>>> Could not find angle parameter: NC - CA - CA >>>> Could not find angle parameter: NC - CA - N* >>>> Could not find angle parameter: CT - N* - CA >>>> Could not find angle parameter: CT - N* - CA >>>> There are missing parameters. >>>> check: Warnings: 1 >>>> Unit is OK. >>>> >>>> saveamberparm myfad fad.top fad.crd >>>> >>>>> >>>>> Checking Unit. >>>> WARNING: The unperturbed charge of the unit: -2.000000 is not zero. >>>> >>>> -- ignoring the warning. >>>> >>>> Building topology. >>>> Building atom parameters. >>>> Building bond parameters. >>>> Could not find bond parameter for: N* - CA >>>> Could not find bond parameter for: N* - CA >>>> Building angle parameters. >>>> Could not find angle parameter: NC - CA - CA >>>> Could not find angle parameter: NC - CA - CA >>>> Could not find angle parameter: CA - NC - CA >>>> Could not find angle parameter: CA - CA - NC >>>> Could not find angle parameter: CA - N* - CA >>>> Could not find angle parameter: N* - CA - CA >>>> Could not find angle parameter: N* - CA - CA >>>> Could not find angle parameter: N* - CA - CA >>>> Could not find angle parameter: O - C - CA >>>> Could not find angle parameter: C - CA - NC >>>> Could not find angle parameter: NA - C - CA >>>> Could not find angle parameter: NC - C - NA >>>> Could not find angle parameter: NC - CA - CA >>>> Could not find angle parameter: NC - CA - N* >>>> Could not find angle parameter: CT - N* - CA >>>> Could not find angle parameter: CT - N* - CA >>>> Building proper torsion parameters. >>>> ** No torsion terms for CA-CA-N*-CA >>>> ** No torsion terms for CA-N*-CA-CA >>>> ** No torsion terms for CA-N*-CA-CA >>>> ** No torsion terms for NC-CA-N*-CA >>>> ** No torsion terms for CT-N*-CA-CA >>>> ** No torsion terms for CT-N*-CA-NC >>>> ** No torsion terms for CT-N*-CA-CA >>>> ** No torsion terms for CT-N*-CA-CA >>>> Building improper torsion parameters. >>>> total 12 improper torsions applied >>>> Building H-Bond parameters. >>>> Parameter file was not saved. >>>> >>>> How can I deal with these problems of angle parameters and torsion >>>> terms? >>>> >>>> Thanks, >>>> Best regards, >>>> >>>> -- >>>> Shahid. >>>> >>> > > > _______________________________________________ > AMBER mailing list > AMBER.ambermd.org > http://lists.ambermd.org/mailman/listinfo/amber > _______________________________________________ AMBER mailing list AMBER.ambermd.org http://lists.ambermd.org/mailman/listinfo/amberReceived on Tue Dec 01 2009 - 04:00:03 PST