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-- 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 Mon Nov 30 2009 - 08:00:02 PST