AMBER Archive (2009)

Subject: [AMBER] problem with FAD in tleap

From: M. Shahid (mohammad.shahid_at_gmail.com)
Date: Mon Nov 30 2009 - 06:17:09 CST

Hi,

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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