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.
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Received on Sun Apr 04 2010 - 23:00:02 PDT
