Hello Everyone
i am new to Amber and facing some problem kindly help me...
For simulation of docked complex i have prepared my ligand structure using
xleap even then I am having error..
Error is :
tleap
-I: Adding /root/amber10/dat/leap/prep to search path.
-I: Adding /root/amber10/dat/leap/lib to search path.
-I: Adding /root/amber10/dat/leap/parm to search path.
-I: Adding /root/amber10/dat/leap/cmd to search path.
Welcome to LEaP!
(no leaprc in search path)
> source leaprc.ff99SB
----- Source: /root/amber10/dat/leap/cmd/leaprc.ff99SB
----- Source of /root/amber10/dat/leap/cmd/leaprc.ff99SB done
Log file: ./leap.log
Loading parameters: /root/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: /root/amber10/dat/leap/parm/frcmod.ff99SB
Reading force field modification type file (frcmod)
Reading title:
Modification/update of parm99.dat (Hornak & Simmerling)
Loading library: /root/amber10/dat/leap/lib/all_nucleic94.lib
Loading library: /root/amber10/dat/leap/lib/all_amino94.lib
Loading library: /root/amber10/dat/leap/lib/all_aminoct94.lib
Loading library: /root/amber10/dat/leap/lib/all_aminont94.lib
Loading library: /root/amber10/dat/leap/lib/ions94.lib
Loading library: /root/amber10/dat/leap/lib/solvents.lib
> source leaprc.gaff
----- Source: /root/amber10/dat/leap/cmd/leaprc.gaff
----- Source of /root/amber10/dat/leap/cmd/leaprc.gaff done
Log file: ./leap.log
Loading parameters: /root/amber10/dat/leap/parm/gaff.dat
Reading title:
AMBER General Force Field for organic mol., add. info. at the end (June,
2003)
> loadamberparams ligj.frcmod
Loading parameters: ./ligj.frcmod
Reading force field modification type file (frcmod)
Reading title:
remark goes here
> loadoff ligj.lib
Loading library: ./ligj.lib
> c = loadpdb AD.pdb
Loading PDB file: ./AD.pdb
Unknown residue: UNK number: 373 type: Terminal/last
..relaxing end constraints to try for a dbase match
-no luck
Created a new atom named: HD1 within residue: .R<HIE 283>
Created a new atom named: HD1 within residue: .R<HIE 299>
Creating new UNIT for residue: UNK sequence: 374
Created a new atom named: C1 within residue: .R<UNK 374>
Created a new atom named: C2 within residue: .R<UNK 374>
Created a new atom named: C3 within residue: .R<UNK 374>
Created a new atom named: C4 within residue: .R<UNK 374>
Created a new atom named: C5 within residue: .R<UNK 374>
Created a new atom named: C6 within residue: .R<UNK 374>
Created a new atom named: C7 within residue: .R<UNK 374>
Created a new atom named: C8 within residue: .R<UNK 374>
Created a new atom named: C9 within residue: .R<UNK 374>
Created a new atom named: C10 within residue: .R<UNK 374>
Created a new atom named: C11 within residue: .R<UNK 374>
Created a new atom named: C12 within residue: .R<UNK 374>
Created a new atom named: C13 within residue: .R<UNK 374>
Created a new atom named: N1 within residue: .R<UNK 374>
Created a new atom named: N2 within residue: .R<UNK 374>
Created a new atom named: O1 within residue: .R<UNK 374>
Created a new atom named: O2 within residue: .R<UNK 374>
Created a new atom named: O3 within residue: .R<UNK 374>
Created a new atom named: O4 within residue: .R<UNK 374>
Created a new atom named: H1 within residue: .R<UNK 374>
Created a new atom named: H2 within residue: .R<UNK 374>
Created a new atom named: H3 within residue: .R<UNK 374>
Created a new atom named: H4 within residue: .R<UNK 374>
Created a new atom named: H5 within residue: .R<UNK 374>
Created a new atom named: H6 within residue: .R<UNK 374>
Created a new atom named: H7 within residue: .R<UNK 374>
Created a new atom named: H8 within residue: .R<UNK 374>
Created a new atom named: H9 within residue: .R<UNK 374>
Created a new atom named: H10 within residue: .R<UNK 374>
Created a new atom named: H11 within residue: .R<UNK 374>
Created a new atom named: H17 within residue: .R<UNK 374>
Created a new atom named: H18 within residue: .R<UNK 374>
Created a new atom named: C45 within residue: .R<UNK 374>
Created a new atom named: C46 within residue: .R<UNK 374>
Created a new atom named: C47 within residue: .R<UNK 374>
Created a new atom named: C48 within residue: .R<UNK 374>
Created a new atom named: C49 within residue: .R<UNK 374>
Created a new atom named: C50 within residue: .R<UNK 374>
Created a new atom named: H51 within residue: .R<UNK 374>
Created a new atom named: H52 within residue: .R<UNK 374>
Created a new atom named: H53 within residue: .R<UNK 374>
Created a new atom named: H54 within residue: .R<UNK 374>
Created a new atom named: H55 within residue: .R<UNK 374>
Created a new atom named: H56 within residue: .R<UNK 374>
Created a new atom named: H57 within residue: .R<UNK 374>
Created a new atom named: H58 within residue: .R<UNK 374>
Created a new atom named: H59 within residue: .R<UNK 374>
Created a new atom named: H60 within residue: .R<UNK 374>
Created a new atom named: H61 within residue: .R<UNK 374>
Created a new atom named: H62 within residue: .R<UNK 374>
Created a new atom named: H63 within residue: .R<UNK 374>
Created a new atom named: H64 within residue: .R<UNK 374>
Created a new atom named: H65 within residue: .R<UNK 374>
Created a new atom named: H66 within residue: .R<UNK 374>
Created a new atom named: H67 within residue: .R<UNK 374>
Created a new atom named: H68 within residue: .R<UNK 374>
Created a new atom named: H69 within residue: .R<UNK 374>
Created a new atom named: H70 within residue: .R<UNK 374>
Created a new atom named: H71 within residue: .R<UNK 374>
Created a new atom named: H72 within residue: .R<UNK 374>
Created a new atom named: H73 within residue: .R<UNK 374>
total atoms in file: 5892
Leap added 2 missing atoms according to residue templates:
2 H / lone pairs
The file contained 63 atoms not in residue templates
> solvatebox c TIP3PBOX 10
(using default radius 1.500000 for C1)
(using default radius 1.500000 for C2)
(using default radius 1.500000 for C3)
(using default radius 1.500000 for C4)
(using default radius 1.500000 for C5)
(using default radius 1.500000 for C6)
(using default radius 1.500000 for C7)
(using default radius 1.500000 for C8)
(using default radius 1.500000 for C9)
(using default radius 1.500000 for C10)
(using default radius 1.500000 for C11)
(using default radius 1.500000 for C12)
(using default radius 1.500000 for C13)
(using default radius 1.500000 for N1)
(using default radius 1.500000 for N2)
(using default radius 1.500000 for O1)
(using default radius 1.500000 for O2)
(using default radius 1.500000 for O3)
(using default radius 1.500000 for O4)
(using default radius 1.500000 for C45)
(using default radius 1.500000 for C46)
(using default radius 1.500000 for C47)
(using default radius 1.500000 for C48)
(using default radius 1.500000 for C49)
(using default radius 1.500000 for C50)
Solute vdw bounding box: 49.836 75.225 61.521
Total bounding box for atom centers: 69.836 95.225 81.521
Solvent unit box: 18.774 18.774 18.774
(using default radius 1.500000 for C1)
(using default radius 1.500000 for C2)
(using default radius 1.500000 for C3)
(using default radius 1.500000 for C4)
(using default radius 1.500000 for C5)
(using default radius 1.500000 for C6)
(using default radius 1.500000 for C7)
(using default radius 1.500000 for C8)
(using default radius 1.500000 for C9)
(using default radius 1.500000 for C10)
(using default radius 1.500000 for C11)
(using default radius 1.500000 for C12)
(using default radius 1.500000 for C13)
(using default radius 1.500000 for N1)
(using default radius 1.500000 for N2)
(using default radius 1.500000 for O1)
(using default radius 1.500000 for O2)
(using default radius 1.500000 for O3)
(using default radius 1.500000 for O4)
(using default radius 1.500000 for C45)
(using default radius 1.500000 for C46)
(using default radius 1.500000 for C47)
(using default radius 1.500000 for C48)
(using default radius 1.500000 for C49)
(using default radius 1.500000 for C50)
Total vdw box size: 72.559 98.214 84.432 angstroms.
Volume: 601687.034 A^3
Mass > 298144.710 amu, Density > 0.823 g/cc
(type - hence mass - of one or more atoms could not be found)
Added 14237 residues.
> saveamberparm c ADlig.prmtop ADlig.inpcrd
Checking Unit.
WARNING: The unperturbed charge of the unit: -10.000000 is not zero.
FATAL: Atom .R<HIE 283>.A<HD1 18> does not have a type.
FATAL: Atom .R<HIE 299>.A<HD1 18> does not have a type.
FATAL: Atom .R<UNK 374>.A<C1 1> does not have a type.
FATAL: Atom .R<UNK 374>.A<C2 2> does not have a type.
FATAL: Atom .R<UNK 374>.A<C3 3> does not have a type.
FATAL: Atom .R<UNK 374>.A<C4 4> does not have a type.
FATAL: Atom .R<UNK 374>.A<C5 5> does not have a type.
FATAL: Atom .R<UNK 374>.A<C6 6> does not have a type.
FATAL: Atom .R<UNK 374>.A<C7 7> does not have a type.
FATAL: Atom .R<UNK 374>.A<C8 8> does not have a type.
FATAL: Atom .R<UNK 374>.A<C9 9> does not have a type.
FATAL: Atom .R<UNK 374>.A<C10 10> does not have a type.
FATAL: Atom .R<UNK 374>.A<C11 11> does not have a type.
FATAL: Atom .R<UNK 374>.A<C12 12> does not have a type.
FATAL: Atom .R<UNK 374>.A<C13 13> does not have a type.
FATAL: Atom .R<UNK 374>.A<N1 14> does not have a type.
FATAL: Atom .R<UNK 374>.A<N2 15> does not have a type.
FATAL: Atom .R<UNK 374>.A<O1 16> does not have a type.
FATAL: Atom .R<UNK 374>.A<O2 17> does not have a type.
FATAL: Atom .R<UNK 374>.A<O3 18> does not have a type.
FATAL: Atom .R<UNK 374>.A<O4 19> does not have a type.
FATAL: Atom .R<UNK 374>.A<H1 20> does not have a type.
FATAL: Atom .R<UNK 374>.A<H2 21> does not have a type.
FATAL: Atom .R<UNK 374>.A<H3 22> does not have a type.
FATAL: Atom .R<UNK 374>.A<H4 23> does not have a type.
FATAL: Atom .R<UNK 374>.A<H5 24> does not have a type.
FATAL: Atom .R<UNK 374>.A<H6 25> does not have a type.
FATAL: Atom .R<UNK 374>.A<H7 26> does not have a type.
FATAL: Atom .R<UNK 374>.A<H8 27> does not have a type.
FATAL: Atom .R<UNK 374>.A<H9 28> does not have a type.
FATAL: Atom .R<UNK 374>.A<H10 29> does not have a type.
FATAL: Atom .R<UNK 374>.A<H11 30> does not have a type.
FATAL: Atom .R<UNK 374>.A<H17 31> does not have a type.
FATAL: Atom .R<UNK 374>.A<H18 32> does not have a type.
FATAL: Atom .R<UNK 374>.A<C45 33> does not have a type.
FATAL: Atom .R<UNK 374>.A<C46 34> does not have a type.
FATAL: Atom .R<UNK 374>.A<C47 35> does not have a type.
FATAL: Atom .R<UNK 374>.A<C48 36> does not have a type.
FATAL: Atom .R<UNK 374>.A<C49 37> does not have a type.
FATAL: Atom .R<UNK 374>.A<C50 38> does not have a type.
FATAL: Atom .R<UNK 374>.A<H51 39> does not have a type.
FATAL: Atom .R<UNK 374>.A<H52 40> does not have a type.
FATAL: Atom .R<UNK 374>.A<H53 41> does not have a type.
FATAL: Atom .R<UNK 374>.A<H54 42> does not have a type.
FATAL: Atom .R<UNK 374>.A<H55 43> does not have a type.
FATAL: Atom .R<UNK 374>.A<H56 44> does not have a type.
FATAL: Atom .R<UNK 374>.A<H57 45> does not have a type.
FATAL: Atom .R<UNK 374>.A<H58 46> does not have a type.
FATAL: Atom .R<UNK 374>.A<H59 47> does not have a type.
FATAL: Atom .R<UNK 374>.A<H60 48> does not have a type.
FATAL: Atom .R<UNK 374>.A<H61 49> does not have a type.
FATAL: Atom .R<UNK 374>.A<H62 50> does not have a type.
FATAL: Atom .R<UNK 374>.A<H63 51> does not have a type.
FATAL: Atom .R<UNK 374>.A<H64 52> does not have a type.
FATAL: Atom .R<UNK 374>.A<H65 53> does not have a type.
FATAL: Atom .R<UNK 374>.A<H66 54> does not have a type.
FATAL: Atom .R<UNK 374>.A<H67 55> does not have a type.
FATAL: Atom .R<UNK 374>.A<H68 56> does not have a type.
FATAL: Atom .R<UNK 374>.A<H69 57> does not have a type.
FATAL: Atom .R<UNK 374>.A<H70 58> does not have a type.
FATAL: Atom .R<UNK 374>.A<H71 59> does not have a type.
FATAL: Atom .R<UNK 374>.A<H72 60> does not have a type.
FATAL: Atom .R<UNK 374>.A<H73 61> does not have a type.
Failed to generate parameters
Parameter file was not saved.
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Received on Tue Sep 18 2012 - 00:30:03 PDT
