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<C14 14> does not have a type.
FATAL: Atom .R<UNK 374>.A<C15 15> does not have a type.
FATAL: Atom .R<UNK 374>.A<C16 16> does not have a type.
FATAL: Atom .R<UNK 374>.A<C17 17> does not have a type.
FATAL: Atom .R<UNK 374>.A<C18 18> does not have a type.
FATAL: Atom .R<UNK 374>.A<C19 19> does not have a type.
FATAL: Atom .R<UNK 374>.A<N1 20> does not have a type.
FATAL: Atom .R<UNK 374>.A<N2 21> does not have a type.
FATAL: Atom .R<UNK 374>.A<O1 22> does not have a type.
FATAL: Atom .R<UNK 374>.A<O2 23> does not have a type.
FATAL: Atom .R<UNK 374>.A<O3 24> does not have a type.
FATAL: Atom .R<UNK 374>.A<O4 25> does not have a type.
FATAL: Atom .R<UNK 374>.A<H1 26> does not have a type.
FATAL: Atom .R<UNK 374>.A<H2 27> does not have a type.
FATAL: Atom .R<UNK 374>.A<H3 28> does not have a type.
FATAL: Atom .R<UNK 374>.A<H4 29> does not have a type.
FATAL: Atom .R<UNK 374>.A<H5 30> does not have a type.
FATAL: Atom .R<UNK 374>.A<H6 31> does not have a type.
FATAL: Atom .R<UNK 374>.A<H7 32> does not have a type.
FATAL: Atom .R<UNK 374>.A<H8 33> does not have a type.
FATAL: Atom .R<UNK 374>.A<H9 34> does not have a type.
FATAL: Atom .R<UNK 374>.A<H10 35> does not have a type.
FATAL: Atom .R<UNK 374>.A<H11 36> does not have a type.
FATAL: Atom .R<UNK 374>.A<H12 37> does not have a type.
FATAL: Atom .R<UNK 374>.A<H13 38> does not have a type.
FATAL: Atom .R<UNK 374>.A<H14 39> does not have a type.
FATAL: Atom .R<UNK 374>.A<H15 40> does not have a type.
FATAL: Atom .R<UNK 374>.A<H16 41> does not have a type.
FATAL: Atom .R<UNK 374>.A<H17 42> does not have a type.
FATAL: Atom .R<UNK 374>.A<H18 43> does not have a type.
Failed to generate parameters
Parameter file was not saved.
On Tue, Nov 13, 2012 at 9:58 AM, Sumra Wajid Abbasi 30-FBAS/MSBI/F09 <
sumra.msbi30.iiu.edu.pk> wrote:
> Dear Jason
>
> I have tried what u suggested but again I am receiving same fatal error.
>
>
> drsiklinux1:~ # export AMBERHOME=/root/amber12
> drsiklinux1:~ # export PATH=$PATH:$AMBERHOME/bin
> drsiklinux1:~ # cd $AMBERHOME/bin
> drsiklinux1:~/amber12/bin # antechamber -i lig1.pdb -fi pdb -o lig1.mol2
> -fo mol2 -c bcc -s 2
> Running: /root/amber12/bin/bondtype -j full -i ANTECHAMBER_BOND_TYPE.AC0
> -o ANTECHAMBER_BOND_TYPE.AC -f ac
>
> Running: /root/amber12/bin/atomtype -i ANTECHAMBER_AC.AC0 -o
> ANTECHAMBER_AC.AC -p gaff
> Total number of electrons: 178; net charge: 0
>
> Running: /root/amber12/bin/sqm -O -i sqm.in -o sqm.out
>
> Running: /root/amber12/bin/am1bcc -i ANTECHAMBER_AM1BCC_PRE.AC -o
> ANTECHAMBER_AM1BCC.AC -f ac -p /root/amber12/dat/antechamber/BCCPARM.DAT
> -s 2 -j 1
>
> Running: /root/amber12/bin/atomtype -f ac -p bcc -o ANTECHAMBER_AM1BCC.AC-i
> ANTECHAMBER_AM1BCC_PRE.AC
>
> drsiklinux1:~/amber12/bin # parmchk -i lig1.mol2 -f mol2 -o lig1.frcmod
> drsiklinux1:~/amber12/bin # tleap
> -I: Adding /root/amber12/dat/leap/prep to search path.
> -I: Adding /root/amber12/dat/leap/lib to search path.
> -I: Adding /root/amber12/dat/leap/parm to search path.
> -I: Adding /root/amber12/dat/leap/cmd to search path.
>
> Welcome to LEaP!
> (no leaprc in search path)
> > source leaprc.ff99SB
> ----- Source: /root/amber12/dat/leap/cmd/leaprc.ff99SB
> ----- Source of /root/amber12/dat/leap/cmd/leaprc.ff99SB done
> Log file: ./leap.log
> Loading parameters: /root/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: /root/amber12/dat/leap/parm/frcmod.ff99SB
> Reading force field modification type file (frcmod)
> Reading
> title:
>
> Modification/update of parm99.dat (Hornak &
> Simmerling)
>
> Loading library:
> /root/amber12/dat/leap/lib/all_nucleic94.lib
>
> Loading library:
> /root/amber12/dat/leap/lib/all_amino94.lib
>
> Loading library:
> /root/amber12/dat/leap/lib/all_aminoct94.lib
>
> Loading library:
> /root/amber12/dat/leap/lib/all_aminont94.lib
>
> Loading library:
> /root/amber12/dat/leap/lib/ions94.lib
>
> Loading library:
> /root/amber12/dat/leap/lib/solvents.lib
>
> > source
> leaprc.gaff
>
> ----- Source:
> /root/amber12/dat/leap/cmd/leaprc.gaff
>
> ----- Source of /root/amber12/dat/leap/cmd/leaprc.gaff
> done
>
> Log file: ./leap.log
> Loading parameters: /root/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
> > SUS=loadmol2 lig1.mol2
>
> Loading Mol2 file: ./lig1.mol2
> Reading MOLECULE named UNK
> > list
> ACE ALA ARG ASH ASN ASP CALA
> CARG
> CASN CASP CCYS CCYX CGLN CGLU CGLY
> CHCL3BOX
> CHID CHIE CHIP CHIS CILE CIO CLEU
> CLYS
> CMET CPHE CPRO CSER CTHR CTRP CTYR
> CVAL
> CYM CYS CYX Cl- Cs+ DA DA3
> DA5
> DAN DC DC3 DC4 DC5 DCN DG
> DG3
> DG5 DGN DT DT3 DT5 DTN GLH
> GLN
> GLU GLY HID HIE HIP HIS HOH
> IB
> ILE K+ LEU LYN LYS Li+ MEOHBOX
> MET
> MG2 NALA NARG NASN NASP NCYS NCYX
> NGLN
> NGLU NGLY NHE NHID NHIE NHIP NHIS
> NILE
> NLEU NLYS NMABOX NME NMET NPHE NPRO
> NSER
> NTHR NTRP NTYR NVAL Na+ PHE PL3
> POL3BOX
> PRO QSPCFWBOX RA RA3 RA5 RAN RC
> RC3
> RC5 RCN RG RG3 RG5 RGN RU
> RU3
> RU5 RUN Rb+ SER SPC SPCBOX SPCFWBOX
> SPF
> SPG SUS T4E THR TIP3PBOX TIP3PFBOX TIP4PBOX
> TIP4PEWBOX
>
> TIP5PBOX TP3 TP4 TP5 TPF TRP TYR
> VAL
> WAT frcmod99SBgaff parm99
> > check SUS
> Checking 'SUS'....
> Checking parameters for unit 'SUS'.
>
> Checking for bond parameters.
> Checking for angle parameters.
> Unit is OK.
> > loadamberparams lig1.frcmod
> Loading parameters: ./lig1.frcmod
> Reading force field modification type file (frcmod)
> Reading title:
> remark goes here
> > saveoff SUS lig1.lib
>
> Building topology.
> Building atom parameters.
> > saveamberparm SUS lig1.prmtop lig1.inpcrd
>
> Checking Unit.
> Building topology.
> Building atom parameters.
> Building bond parameters.
> Building angle parameters.
> Building proper torsion parameters.
> Building improper torsion parameters.
> total 18 improper torsions applied
> Building H-Bond parameters.
> Not Marking per-residue atom chain types.
> Marking per-residue atom chain types.
> (Residues lacking connect0/connect1 -
> these don't have chain types marked:
>
> res total affected
>
> UNK 1
> )
> (no restraints)
> > quit
> Quit
> drsiklinux1:~/amber12/bin # tleap
> -I: Adding /root/amber12/dat/leap/prep to search path.
> -I: Adding /root/amber12/dat/leap/lib to search path.
> -I: Adding /root/amber12/dat/leap/parm to search path.
> -I: Adding /root/amber12/dat/leap/cmd to search path.
>
> Welcome to LEaP!
> (no leaprc in search path)
> > source leaprc.ff99SB
> ----- Source: /root/amber12/dat/leap/cmd/leaprc.ff99SB
> ----- Source of /root/amber12/dat/leap/cmd/leaprc.ff99SB done
> Log file: ./leap.log
> Loading parameters: /root/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: /root/amber12/dat/leap/parm/frcmod.ff99SB
> Reading force field modification type file (frcmod)
> Reading title:
> Modification/update of parm99.dat (Hornak & Simmerling)
> Loading library: /root/amber12/dat/leap/lib/all_nucleic94.lib
> Loading library: /root/amber12/dat/leap/lib/all_amino94.lib
> Loading library: /root/amber12/dat/leap/lib/all_aminoct94.lib
> Loading library: /root/amber12/dat/leap/lib/all_aminont94.lib
> Loading library: /root/amber12/dat/leap/lib/ions94.lib
> Loading library: /root/amber12/dat/leap/lib/solvents.lib
> > source leaprc.gaff
> ----- Source: /root/amber12/dat/leap/cmd/leaprc.gaff
> ----- Source of /root/amber12/dat/leap/cmd/leaprc.gaff done
> Log file: ./leap.log
> Loading parameters: /root/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 lig1.frcmod
> Loading parameters: ./lig1.frcmod
> Reading force field modification type file (frcmod)
> Reading title:
> remark goes here
> > loadoff lig1.lib
> Loading library: ./lig1.lib
> > X=loadpdb B22ASMT.pdb
> Loading PDB file: ./B22ASMT.pdb
> Unknown residue: UNK number: 373 type: Terminal/last
> ..relaxing end constraints to try for a dbase match
> -no luck
> 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: C14 within residue: .R<UNK 374>
> Created a new atom named: C15 within residue: .R<UNK 374>
> Created a new atom named: C16 within residue: .R<UNK 374>
> Created a new atom named: C17 within residue: .R<UNK 374>
> Created a new atom named: C18 within residue: .R<UNK 374>
> Created a new atom named: C19 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: H12 within residue: .R<UNK 374>
> Created a new atom named: H13 within residue: .R<UNK 374>
> Created a new atom named: H14 within residue: .R<UNK 374>
> Created a new atom named: H15 within residue: .R<UNK 374>
> Created a new atom named: H16 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>
> total atoms in file: 5874
> The file contained 43 atoms not in residue templates
> > solvatebox X TIP3PBOX8
> solvateBox: Argument #2 is type String must be of type: [unit]
> usage: solvateBox <solute> <solvent> <buffer> [iso] [closeness]
>
> > solvatebox X TIP3PBOX 8
> (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 C14)
> (using default radius 1.500000 for C15)
> (using default radius 1.500000 for C16)
> (using default radius 1.500000 for C17)
> (using default radius 1.500000 for C18)
> (using default radius 1.500000 for C19)
> (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)
> Solute vdw bounding box: 49.836 75.225 61.521
> Total bounding box for atom centers: 65.836 91.225 77.521
> 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 C14)
> (using default radius 1.500000 for C15)
> (using default radius 1.500000 for C16)
> (using default radius 1.500000 for C17)
> (using default radius 1.500000 for C18)
> (using default radius 1.500000 for C19)
> (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)
> Total vdw box size: 68.947 94.119 80.771 angstroms.
> Volume: 524136.845 A^3
> Mass > 254059.558 amu, Density > 0.805 g/cc
> (type - hence mass - of one or more atoms could not be found)
> Added 11790 residues.
> > charge X
> Total unperturbed charge: -10.000000
> Total perturbed charge: -10.000000
> > addIons X Na+ 0
> 10 Na+ ions required to neutralize.
> Adding 10 counter ions to "X" using 1A grid
> Used default radius 1.50 for 43 atoms
>
> Grid extends from solute vdw + 4.15 to 10.15
> Resolution: 1.00 Angstrom.
> grid build: 0 sec
> Solvent present: replacing closest with ion
> when steric overlaps occur
> Calculating grid charges
> charges: 13 sec
> (Replacing solvent molecule)
> Placed Na+ in X at (20.00, 4.91, -23.36).
> (Replacing solvent molecule)
> Placed Na+ in X at (15.77, -24.36, -5.52).
> (Replacing solvent molecule)
> Placed Na+ in X at (7.45, -29.54, 10.13).
> (Replacing solvent molecule)
> Placed Na+ in X at (-15.35, 7.74, 4.86).
> (Replacing solvent molecule)
> Placed Na+ in X at (14.41, 17.81, 8.30).
> (Replacing solvent molecule)
> Placed Na+ in X at (2.53, -26.56, -27.84).
> (Replacing solvent molecule)
> Placed Na+ in X at (20.75, -8.38, -15.20).
> (Replacing solvent molecule)
> Placed Na+ in X at (0.20, -25.91, 18.53).
> (Replacing solvent molecule)
> Placed Na+ in X at (9.48, 13.80, 27.57).
> (Replacing solvent molecule)
> Placed Na+ in X at (21.83, -13.67, 3.81).
>
> Done adding ions.
> > saveamberparm X B22ASMT.prmtop B22ASMT.inpcrd
> Checking Unit.
>
> 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<C14 14> does not have a type.
> FATAL: Atom .R<UNK 374>.A<C15 15> does not have a type.
> FATAL: Atom .R<UNK 374>.A<C16 16> does not have a type.
> FATAL: Atom .R<UNK 374>.A<C17 17> does not have a type.
> FATAL: Atom .R<UNK 374>.A<C18 18> does not have a type.
> FATAL: Atom .R<UNK 374>.A<C19 19> does not have a type.
> FATAL: Atom .R<UNK 374>.A<N1 20> does not have a type.
> FATAL: Atom .R<UNK 374>.A<N2 21> does not have a type.
> FATAL: Atom .R<UNK 374>.A<O1 22> does not have a type.
> FATAL: Atom .R<UNK 374>.A<O2 23> does not have a type.
> FATAL: Atom .R<UNK 374>.A<O3 24> does not have a type.
> FATAL: Atom .R<UNK 374>.A<O4 25> does not have a type.
> FATAL: Atom .R<UNK 374>.A<H1 26> does not have a type.
> FATAL: Atom .R<UNK 374>.A<H2 27> does not have a type.
> FATAL: Atom .R<UNK 374>.A<H3 28> does not have a type.
> FATAL: Atom .R<UNK 374>.A<H4 29> does not have a type.
> FATAL: Atom .R<UNK 374>.A<H5 30> does not have a type.
> FATAL: Atom .R<UNK 374>.A<H6 31> does not have a type.
> FATAL: Atom .R<UNK 374>.A<H7 32> does not have a type.
> FATAL: Atom .R<UNK 374>.A<H8 33> does not have a type.
> FATAL: Atom .R<UNK 374>.A<H9 34> does not have a type.
> FATAL: Atom .R<UNK 374>.A<H10 35> does not have a type.
> FATAL: Atom .R<UNK 374>.A<H11 36> does not have a type.
> FATAL: Atom .R<UNK 374>.A<H12 37> does not have a type.
> FATAL: Atom .R<UNK 374>.A<H13 38> does not have a type.
> FATAL: Atom .R<UNK 374>.A<H14 39> does not have a type.
> FATAL: Atom .R<UNK 374>.A<H15 40> does not have a type.
> FATAL: Atom .R<UNK 374>.A<H16 41> does not have a type.
> FATAL: Atom .R<UNK 374>.A<H17 42> does not have a type.
> FATAL: Atom .R<UNK 374>.A<H18 43> does not have a type.
> Failed to generate parameters
> Parameter file was not saved.
> >
>
>
>
> On Tue, Nov 13, 2012 at 9:44 AM, Sumra Wajid Abbasi 30-FBAS/MSBI/F09 <
> sumra.msbi30.iiu.edu.pk> wrote:
>
>> Dear Jason
>>
>> thank you..
>>
>> regards
>> Sumra
>>
>>
>>
>> On Mon, Nov 12, 2012 at 5:25 PM, Jason Swails <jason.swails.gmail.com>wrote:
>>
>>> On Mon, Nov 12, 2012 at 4:05 AM, Sumra Wajid Abbasi 30-FBAS/MSBI/F09 <
>>> sumra.msbi30.iiu.edu.pk> wrote:
>>> >
>>> > 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
>>> >
>>>
>>> You do not have a library file for the UNK residue. Or if you do, you
>>> did
>>> not load it into tleap. Therefore, tleap has no idea what this residue
>>> is,
>>> and it will be unable to load the parameters for it.
>>>
>>> Please see http://ambermd.org/tutorials/basic/tutorial4b/ for using
>>> antechamber (which is typically used to help generate parameters and
>>> charges for *just* a single residue like UNK in this instance).
>>>
>>> All of your later error messages come from this mistake.
>>>
>>> Good luck,
>>> Jason
>>>
>>> --
>>> Jason M. Swails
>>> Quantum Theory Project,
>>> University of Florida
>>> Ph.D. Candidate
>>> 352-392-4032
>>> _______________________________________________
>>> AMBER mailing list
>>> AMBER.ambermd.org
>>> http://lists.ambermd.org/mailman/listinfo/amber
>>>
>>
>>
>
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Received on Mon Nov 12 2012 - 21:30:03 PST
