Dear Sir,
when i am loading my dna in tleap. i am getting following errors. its has
Thymine dimers. so, i went through parameter generation, and is
successfully loaded but i am getting following errors in phosphate group.
plz help me on this subject.
tleap
-I: Adding /opt/apps/amber/amber12/dat/leap/prep to search path.
-I: Adding /opt/apps/amber/amber12/dat/leap/lib to search path.
-I: Adding /opt/apps/amber/amber12/dat/leap/parm to search path.
-I: Adding /opt/apps/amber/amber12/dat/leap/cmd to search path.
Welcome to LEaP!
(no leaprc in search path)
> source leaprc.ff99SB
----- Source: /opt/apps/amber/amber12/dat/leap/cmd/leaprc.ff99SB
----- Source of /opt/apps/amber/amber12/dat/leap/cmd/leaprc.ff99SB done
Log file: ./leap.log
Loading parameters: /opt/apps/amber/amber12/dat/leap/parm/parm99.dat
Reading title:
PARM99 for DNA,RNA,AA, organic molecules, TIP3P wat. Polariz.& LP
incl.02/04/99
Loading parameters: /opt/apps/amber/amber12/dat/leap/parm/frcmod.ff99SB
Reading force field modification type file (frcmod)
Reading title:
Modification/update of parm99.dat (Hornak & Simmerling)
Loading library: /opt/apps/amber/amber12/dat/leap/lib/all_nucleic94.lib
Loading library: /opt/apps/amber/amber12/dat/leap/lib/all_amino94.lib
Loading library: /opt/apps/amber/amber12/dat/leap/lib/all_aminoct94.lib
Loading library: /opt/apps/amber/amber12/dat/leap/lib/all_aminont94.lib
Loading library: /opt/apps/amber/amber12/dat/leap/lib/ions94.lib
Loading library: /opt/apps/amber/amber12/dat/leap/lib/solvents.lib
> source leaprc.gaff
----- Source: /opt/apps/amber/amber12/dat/leap/cmd/leaprc.gaff
----- Source of /opt/apps/amber/amber12/dat/leap/cmd/leaprc.gaff done
Log file: ./leap.log
Loading parameters: /opt/apps/amber/amber12/dat/leap/parm/gaff.dat
Reading title:
AMBER General Force Field for organic molecules (Version 1.4, March 2010)
add. info. at the end
> loadamberparams TTD.frcmod
Could not open file TTD.frcmod: not found
> loadOff ttd.lib
Loading library: ./ttd.lib
> loadamberparams TTD.frcmod
Loading parameters: ./TTD.frcmod
Reading force field modification type file (frcmod)
Reading title:
remark goes here
> a = loadpdb "dna_amber5.pdb"
Loading PDB file: ./dna_amber5.pdb
One sided connection. Residue: Displayed missing connect0 atom.
Added missing heavy atom: .R<TTD 473>.A<O66 66>
One sided connection. Residue: default_name missing connect1 atom.
Created a new atom named: P within residue: .R<DG5 478>
Created a new atom named: O1P within residue: .R<DG5 478>
Created a new atom named: O2P within residue: .R<DG5 478>
Added missing heavy atom: .R<DC 479>.A<C5' 5>
Added missing heavy atom: .R<DC 479>.A<C4' 8>
Added missing heavy atom: .R<DC 479>.A<O4' 10>
Added missing heavy atom: .R<DC 479>.A<C3' 25>
Added missing heavy atom: .R<DC 479>.A<C1' 11>
Added missing heavy atom: .R<DC 479>.A<C2' 27>
Added missing heavy atom: .R<DC 479>.A<O3' 30>
Added missing heavy atom: .R<DC 479>.A<N1 13>
Added missing heavy atom: .R<DC 479>.A<C6 14>
Added missing heavy atom: .R<DC 479>.A<C2 23>
Added missing heavy atom: .R<DC 479>.A<C5 16>
Added missing heavy atom: .R<DC 479>.A<N3 22>
Added missing heavy atom: .R<DC 479>.A<O2 24>
Added missing heavy atom: .R<DC 479>.A<C4 18>
Added missing heavy atom: .R<DC 479>.A<N4 19>
Added missing heavy atom: .R<DT 480>.A<C3' 27>
Added missing heavy atom: .R<DT 480>.A<C4' 8>
Added missing heavy atom: .R<DT 480>.A<C2' 29>
Added missing heavy atom: .R<DT 480>.A<C5' 5>
Added missing heavy atom: .R<DT 480>.A<O4' 10>
Added missing heavy atom: .R<DT 480>.A<C1' 11>
Added missing heavy atom: .R<DT 480>.A<O5' 4>
Added missing heavy atom: .R<DT 480>.A<N1 13>
Added missing heavy atom: .R<DT 480>.A<P 1>
Added missing heavy atom: .R<DT 480>.A<C6 14>
Added missing heavy atom: .R<DT 480>.A<C2 25>
Added missing heavy atom: .R<DT 480>.A<O1P 2>
Added missing heavy atom: .R<DT 480>.A<O2P 3>
Added missing heavy atom: .R<DT 480>.A<C5 16>
Added missing heavy atom: .R<DT 480>.A<N3 23>
Added missing heavy atom: .R<DT 480>.A<O2 26>
Added missing heavy atom: .R<DT 480>.A<C7 17>
Added missing heavy atom: .R<DT 480>.A<C4 21>
Added missing heavy atom: .R<DT 480>.A<O4 22>
total atoms in file: 390
Leap added 279 missing atoms according to residue templates:
35 Heavy
244 H / lone pairs
The file contained 3 atoms not in residue templates
>
--
*Regards,
Suresh Satpati*
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Tue Apr 09 2013 - 02:00:02 PDT
