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 - 21:00:02 PST
