I think this is only the problem of atom type, so you can run antechamber.
On Mon, Apr 5, 2010 at 11:12 AM, Asfa Ali <asfa.iisc.gmail.com> wrote:
> Hi,
>
> I want to carry out simulation of RNA. However when I am loading the
> molecule in tleap, it is showing the following error and I am not able to
> save it.
>
>
> tleap -s -f leaprc.ff99bsc0
> -I: Adding /root/amber11/dat/leap/prep to search path.
> -I: Adding /root/amber11/dat/leap/lib to search path.
> -I: Adding /root/amber11/dat/leap/parm to search path.
> -I: Adding /root/amber11/dat/leap/cmd to search path.
> -s: Ignoring startup file: leaprc
> -f: Source leaprc.ff99bsc0.
>
> Welcome to LEaP!
> Sourcing: /root/amber11/dat/leap/cmd/leaprc.ff99bsc0
> Log file: ./leap.log
> Loading parameters: /root/amber11/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/amber11/dat/leap/parm/frcmod.ff99SB
> Reading force field modification type file (frcmod)
> Reading title:
> Modification/update of parm99.dat (Hornak & Simmerling)
> Loading parameters: /root/amber11/dat/leap/parm/frcmod.parmbsc0
> Reading force field modification type file (frcmod)
> Reading title:
> modifies parm99 for nucleic acids: see http://mmb.pcb.ub.es/PARMBSC0/
> Loading library: /root/amber11/dat/leap/lib/all_nucleic94.lib
> Loading library: /root/amber11/dat/leap/lib/all_amino94.lib
> Loading library: /root/amber11/dat/leap/lib/all_aminoct94.lib
> Loading library: /root/amber11/dat/leap/lib/all_aminont94.lib
> Loading library: /root/amber11/dat/leap/lib/DNA_CI.lib
> Loading library: /root/amber11/dat/leap/lib/ions94.lib
> Loading library: /root/amber11/dat/leap/lib/solvents.lib
> > rna=loadpdb "/localhome/macromolecules/2kbp/2kbp_f.pdb"
> Loading PDB file: /localhome/macromolecules/2kbp/2kbp_f.pdb
> Created a new atom named: HO'5 within residue: .R<RU5 1>
> Created a new atom named: HO'3 within residue: .R<RU3 12>
> Created a new atom named: HO'5 within residue: .R<RU5 13>
> Created a new atom named: HO'3 within residue: .R<RU3 24>
> total atoms in file: 778
> Leap added 4 missing atoms according to residue templates:
> 4 H / lone pairs
> The file contained 4 atoms not in residue templates
> Since added/missing = extra, there is a high probability
> of atoms with 'incorrect' names; you may want to
> use addPdbAtomMap to map these names, or change in file
> > saveamberparm rna 2kbp.prmtop 2kbp.inpcrd
> Checking Unit.
> WARNING: The unperturbed charge of the unit: -22.000000 is not zero.
> FATAL: Atom .R<RU5 1>.A<HO'5 29> does not have a type.
> FATAL: Atom .R<RU3 12>.A<HO'3 32> does not have a type.
> FATAL: Atom .R<RU5 13>.A<HO'5 29> does not have a type.
> FATAL: Atom .R<RU3 24>.A<HO'3 32> does not have a type.
> Failed to generate parameters
> Parameter file was not saved.
>
>
> How to solve it?
> Plz help.
>
> Thanks,
> Asfa.
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
With best regards
Dr. Shamoon Ahmad Siddiqui
DBT Postdoctoral Fellow
Molecular Biophysics Unit
Indian Institute of Science
Bangalore-560012, India
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Sun Apr 04 2010 - 23:00:03 PDT
