my leap input is
source leaprc.ff99
set default PBradii bondi
PTH1 = loadPdb PTH1.pdb
charge PTH1
saveAmberParm PTH1 PTH1.top PTH1.crd
quit
and out put is
Welcome to LEaP!
(no leaprc in search path)
Sourcing: ./zmodel.leap.scrpt
----- Source: /home/cdrinmr1/amber9/dat/leap/cmd/leaprc.ff99
----- Source of /home/cdrinmr1/amber9/dat/leap/cmd/leaprc.ff99 done
Log file: ./leap.log
Loading parameters: /home/cdrinmr1/amber9/dat/leap/parm/parm99.dat
Reading title:
PARM99 for DNA,RNA,AA, organic molecules, TIP3P wat. Polariz.& LP incl.02/04/99
Loading library: /home/cdrinmr1/amber9/dat/leap/lib/all_nucleic94.lib
Loading library: /home/cdrinmr1/amber9/dat/leap/lib/all_amino94.lib
Loading library: /home/cdrinmr1/amber9/dat/leap/lib/all_aminoct94.lib
Loading library: /home/cdrinmr1/amber9/dat/leap/lib/all_aminont94.lib
Loading library: /home/cdrinmr1/amber9/dat/leap/lib/ions94.lib
Loading library: /home/cdrinmr1/amber9/dat/leap/lib/solvents.lib
Using Bondi radii
Loading PDB file: ./PTH1.pdb
Added missing heavy atom: .R<CTRP 191>.A<OXT 25>
total atoms in file: 2681
Leap added 226 missing atoms according to residue templates:
1 Heavy
225 H / lone pairs
Total unperturbed charge: 6.000000
Total perturbed charge: 6.000000
Checking Unit.
WARNING: The unperturbed charge of the unit: 6.000000 is not zero.
-- ignoring the warning.
Building topology.
Building atom parameters.
Building bond parameters.
Building angle parameters.
Building proper torsion parameters.
Building improper torsion parameters.
total 581 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
CTRP 1
NMET 1
)
(no restraints)
Quit
struct_calc/amber>
my pdb file..has the form
ATOM 1 N MET 1 1.211 26.605 4.593 1.00 0.00 N
-----------------------------------------------------------------------------------
ATOM 2681 HH2 TRP 191 -11.091 -2.406 6.682 1.00 0.00 H
TER
END
a total of 1-191 residues.
now the leap is not generating the topology file and restraint file.
how to solve the problem.
On 7/24/07, Carlos Simmerling <carlos.simmerling.gmail.com> wrote:
> could you show your leap input?
>
> On 7/24/07, Prem Prakash Pathak <prempolymer.gmail.com> wrote:
> > Hi
> > I am runing the tleap
> > but at the end i get following message
> > Added missing heavy atom: .R<CTRP 191>.A<OXT 25>
> > total atoms in file: 2681
> > Leap added 226 missing atoms according to residue templates:
> > 1 Heavy
> > 225 H / lone pairs
> > Total unperturbed charge: 6.000000
> > Total perturbed charge: 6.000000
> > ERROR: syntax error
> >
> > Checking Unit.
> > WARNING: The unperturbed charge of the unit: 6.000000 is not zero.
> >
> > -- ignoring the warning.
> >
> > Building topology.
> > Building atom parameters.
> > Building bond parameters.
> > Building angle parameters.
> > Building proper torsion parameters.
> > Building improper torsion parameters.
> > total 581 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
> >
> > CTRP 1
> > NMET 1
> > )
> > (no restraints)
> > Quit
> > struct_calc/amber>
> >
> > and finaly i am not getting the topology file and the restraint file
> >
> > what could be the problem
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Received on Wed Jul 25 2007 - 06:07:45 PDT
