I don't see anything unusual- does the leap.log have more info?
it usually is more helpful than the output.
On 7/25/07, Prem Prakash Pathak <prempolymer.gmail.com> wrote:
> 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 Sun Jul 29 2007 - 06:07:06 PDT
