Hi
Thank you. My amber9 got installed. Now can run tleap.
With new type of problem.
upon running i get following output
I: Adding /home/cdrinmr1/amber9/dat/leap/prep to search path.
-I: Adding /home/cdrinmr1/amber9/dat/leap/lib to search path.
-I: Adding /home/cdrinmr1/amber9/dat/leap/parm to search path.
-I: Adding /home/cdrinmr1/amber9/dat/leap/cmd to search path.
-f: Source zmodel.leap.scrpt.
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: ./PTH.pdb
Created a new atom named: H within residue: .R<NMET 1>
Added missing heavy atom: .R<CTRP 191>.A<OXT 25>
total atoms in file: 2681
Leap added 234 missing atoms according to residue templates:
1 Heavy
233 H / lone pairs
The file contained 1 atoms not in residue templates
Checking Unit.
WARNING: The unperturbed charge of the unit: 13.000000 is not zero.
FATAL: Atom .R<NMET 1>.A<H 20> does not have a type.
Failed to generate parameters
Parameter file was not saved.
Quit
struct_calc/amber>
mine is protein stucture, it is a monomer.
i do not understand why it is showing such a problem.
On 7/23/07, Ross Walker <ross.rosswalker.co.uk> wrote:
>
> > yacc parser.y
> > make[2]: yacc: Command not found
>
> You need to install byacc:
>
> On Redhat EL4 this is:
>
> > rpm -qf /usr/bin/yacc
> byacc-1.9-28
>
> This is normally part of the default installation but in your case it
> obviously wasn't installed by default.
>
> Good luck,
>
> Ross
>
> /\
> \/
> |\oss Walker
>
> | HPC Consultant and Staff Scientist |
> | San Diego Supercomputer Center |
> | Tel: +1 858 822 0854 | EMail:- ross.rosswalker.co.uk |
> | http://www.rosswalker.co.uk | PGP Key available on request |
>
> Note: Electronic Mail is not secure, has no guarantee of delivery, may not
> be read every day, and should not be used for urgent or sensitive issues.
>
>
> -
>
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Received on Wed Jul 25 2007 - 06:07:32 PDT
