AMBER Archive (2009)

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

From: M. Shahid (mohammad.shahid_at_gmail.com)
Date: Tue Dec 01 2009 - 05:54:04 CST

Dear Francois,

All of the problems are resolved now.
I had renamed the residues in FAD but didn't change the number of residues
in the mol2.
Just changed the number of residues from 4 to 1 in the mol2 and everything
went smooth.

Thank you and all who gave the good suggestions.

Best regards, 

--
Shahid.

On Mon, Nov 30, 2009 at 8:15 PM, FyD <fyd_at_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_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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