AMBER Archive (2009)

Subject: Re: [AMBER] problem with FAD in tleap

From: FyD (fyd_at_q4md-forcefieldtools.org)
Date: Mon Nov 30 2009 - 07:02:59 CST

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.

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