Dear Daniel
Thank you so much for your reply and guidance...I have used tutorial B4
previously..but now I will definitely use the A1 tutorial.. hope it would
works for me.. will let you know
kind regards
Sumra
On Tue, Sep 18, 2012 at 4:56 PM, Daniel Roe <daniel.r.roe.gmail.com> wrote:
> Hi,
>
> You will need to generate and load parameters for your ligand (UNK). See
> tutorial A1, http://ambermd.org/tutorials/.
>
> -Dan
>
> On Tuesday, September 18, 2012, Sumra Wajid Abbasi 30-FBAS/MSBI/F09 wrote:
>
> > 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.
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org <javascript:;>
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
> --
> -------------------------
> Daniel R. Roe, PhD
> Department of Medicinal Chemistry
> University of Utah
> 30 South 2000 East, Room 201
> Salt Lake City, UT 84112-5820
> http://home.chpc.utah.edu/~cheatham/
> (801) 587-9652
> (801) 585-9119 (Fax)
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Tue Sep 18 2012 - 06:30:04 PDT
