AMBER Archive (2009)

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

From: FyD (fyd_at_q4md-forcefieldtools.org)
Date: Mon Nov 30 2009 - 13:15:56 CST

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_at_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.

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