---------- Forwarded message ----------
From: suresh satpati <satpatisuresh.gmail.com>
Date: Mon, Apr 8, 2013 at 10:38 AM
Subject: xleap problem
To: amber.ambermd.org
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
> 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 "61.pdb"
Loading PDB file: ./61.pdb
(starting new molecule for chain B)
Added missing heavy atom: .R<CPHE 468>.A<OXT 21>
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<DC3 479>.A<C5' 5>
Added missing heavy atom: .R<DC3 479>.A<C4' 8>
Added missing heavy atom: .R<DC3 479>.A<O4' 10>
Added missing heavy atom: .R<DC3 479>.A<C3' 25>
Added missing heavy atom: .R<DC3 479>.A<C1' 11>
Added missing heavy atom: .R<DC3 479>.A<C2' 27>
Added missing heavy atom: .R<DC3 479>.A<O3' 30>
Added missing heavy atom: .R<DC3 479>.A<N1 13>
Added missing heavy atom: .R<DC3 479>.A<C6 14>
Added missing heavy atom: .R<DC3 479>.A<C2 23>
Added missing heavy atom: .R<DC3 479>.A<C5 16>
Added missing heavy atom: .R<DC3 479>.A<N3 22>
Added missing heavy atom: .R<DC3 479>.A<O2 24>
Added missing heavy atom: .R<DC3 479>.A<C4 18>
Added missing heavy atom: .R<DC3 479>.A<N4 19>
Added missing heavy atom: .R<DT5 480>.A<C3' 25>
Added missing heavy atom: .R<DT5 480>.A<C4' 6>
Added missing heavy atom: .R<DT5 480>.A<C2' 27>
Added missing heavy atom: .R<DT5 480>.A<C5' 3>
Added missing heavy atom: .R<DT5 480>.A<O4' 8>
Added missing heavy atom: .R<DT5 480>.A<C1' 9>
Added missing heavy atom: .R<DT5 480>.A<O5' 2>
Added missing heavy atom: .R<DT5 480>.A<N1 11>
Added missing heavy atom: .R<DT5 480>.A<C6 12>
Added missing heavy atom: .R<DT5 480>.A<C2 23>
Added missing heavy atom: .R<DT5 480>.A<C5 14>
Added missing heavy atom: .R<DT5 480>.A<N3 21>
Added missing heavy atom: .R<DT5 480>.A<O2 24>
Added missing heavy atom: .R<DT5 480>.A<C7 15>
Added missing heavy atom: .R<DT5 480>.A<C4 19>
Added missing heavy atom: .R<DT5 480>.A<O4 20>
total atoms in file: 4097
Leap added 4067 missing atoms according to residue templates:
33 Heavy
4034 H / lone pairs
The file contained 3 atoms not in residue templates
Dear Sir,
i have a problem on loading this uploaded pdb file. hence it has Thymine
dimer i managed to generate parameters for dimer and successfully loaded.
but, i don't know wats the problem in loading phosphote at guanine 478. plz
let me know some solution.
--
*Regards,
Suresh Satpati*
*JRF, **Institute of LifeSciences*
*Bhubneshwar - 751023*
*India
*
*
*
*-Mob. No. +91-9861138427*
--
*Regards,
Suresh Satpati*
*JRF, **Institute of LifeSciences*
*Bhubneshwar - 751023*
*India
*
*
*
*-Mob. No. +91-9861138427*
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- chemical/x-pdb attachment: 5.pdb
Received on Sun Apr 07 2013 - 23:00:02 PDT
