AMBER Archive (2007)

Subject: Re: AMBER: not getting topology and restraint file

From: Prem Prakash Pathak (prempolymer_at_gmail.com)
Date: Wed Jul 25 2007 - 08:45:57 CDT

I checked it once more it has created the topology file and restraint file.
thank you very much.

On 7/25/07, Carlos Simmerling <carlos.simmerling_at_gmail.com> wrote:
> 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_at_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_at_gmail.com> wrote:
> > > could you show your leap input?
> > >
> > > On 7/24/07, Prem Prakash Pathak <prempolymer_at_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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