Hi,
I would like to state my problem in greater details now.
I had docked my ligand with DNA and with the docked output file from
Autodock (converted to pdb), was running tleap commands as folows:
(The parameter & co-ord files of ligand named prp3 was created without any
error)
/localhome$ tleap -f tleap2_2h.in
-I: Adding /root/amber11/dat/leap/prep to search path.
-I: Adding /root/amber11/dat/leap/lib to search path.
-I: Adding /root/amber11/dat/leap/parm to search path.
-I: Adding /root/amber11/dat/leap/cmd to search path.
-f: Source tleap2_2h.in.
Welcome to LEaP!
(no leaprc in search path)
Sourcing: ./tleap2_2h.in
----- Source: /root/amber11/dat/leap/cmd/leaprc.ff99bsc0
----- Source of /root/amber11/dat/leap/cmd/leaprc.ff99bsc0 done
Log file: ./leap.log
Loading parameters: /root/amber11/dat/leap/parm/parm99.dat
Reading title:
PARM99 for DNA,RNA,AA, organic molecules, TIP3P wat. Polariz.& LP
incl.02/04/99
Loading parameters: /root/amber11/dat/leap/parm/frcmod.ff99SB
Reading force field modification type file (frcmod)
Reading title:
Modification/update of parm99.dat (Hornak & Simmerling)
Loading parameters: /root/amber11/dat/leap/parm/frcmod.parmbsc0
Reading force field modification type file (frcmod)
Reading title:
modifies parm99 for nucleic acids: see http://mmb.pcb.ub.es/PARMBSC0/
Loading library: /root/amber11/dat/leap/lib/all_nucleic94.lib
Loading library: /root/amber11/dat/leap/lib/all_amino94.lib
Loading library: /root/amber11/dat/leap/lib/all_aminoct94.lib
Loading library: /root/amber11/dat/leap/lib/all_aminont94.lib
Loading library: /root/amber11/dat/leap/lib/DNA_CI.lib
Loading library: /root/amber11/dat/leap/lib/ions94.lib
Loading library: /root/amber11/dat/leap/lib/solvents.lib
----- Source: /root/amber11/dat/leap/cmd/leaprc.gaff
----- Source of /root/amber11/dat/leap/cmd/leaprc.gaff done
Log file: ./leap.log
Loading parameters: /root/amber11/dat/leap/parm/gaff.dat
Reading title:
AMBER General Force Field for organic mol., add. info. at the end (June,
2003)
Loading parameters: ./prp3.frcmod
Reading force field modification type file (frcmod)
Reading title:
remark goes here
Loading library: ./prp3.lib
Loading PDB file: ./2hy9-l1-lap-com.pdb
-- residue 27: duplicate [ C] atoms (total 44)
-- residue 27: duplicate [ H] atoms (total 2)
-- residue 27: duplicate [ N] atoms (total 8)
Warning: Atom names in each residue should be unique.
(Same-name atoms are handled by using the first
occurrence and by ignoring the rest.
Frequently duplicate atom names stem from alternate
conformations in the PDB file.)
Unknown residue: LIG number: 26 type: Terminal/last
..relaxing end constraints to try for a dbase match
-no luck
Creating new UNIT for residue: LIG sequence: 27
Created a new atom named: C within residue: .R<LIG 27>
Created a new atom named: N within residue: .R<LIG 27>
Created a new atom named: H within residue: .R<LIG 27>
total atoms in file: 663
Leap added 234 missing atoms according to residue templates:
234 H / lone pairs
The file contained 3 atoms not in residue templates
Checking Unit.
WARNING: The unperturbed charge of the unit: -25.000000 is not zero.
FATAL: Atom .R<LIG 27>.A<C 1> does not have a type.
FATAL: Atom .R<LIG 27>.A<N 2> does not have a type.
FATAL: Atom .R<LIG 27>.A<H 3> does not have a type.
Failed to generate parameters
Parameter file was not saved.
Quit
Please help. I am quite new in this field, so kindly tell me the steps to
sort out this problem.
Thanks a lot...
Asfa.
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Received on Tue Apr 13 2010 - 13:00:02 PDT
