AMBER Archive (2009)

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

From: M. Shahid (mohammad.shahid_at_gmail.com)
Date: Mon Nov 30 2009 - 09:54:26 CST

Dear 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

used the parameters

X -N*-CA-X 4 14.50 180.0 2.
CT-N*-CA-CA 1.0 180. 2.

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.

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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