thanks Bill
I added that line after that it is giving the error
[root.localhost new]# tleap -f leaprc.ff99SB
-I: Adding /opt/amber10/dat/leap/prep to search path.
-I: Adding /opt/amber10/dat/leap/lib to search path.
-I: Adding /opt/amber10/dat/leap/parm to search path.
-I: Adding /opt/amber10/dat/leap/cmd to search path.
-f: Source leaprc.ff99SB.
Welcome to LEaP!
(no leaprc in search path)
Sourcing: /opt/amber10/dat/leap/cmd/leaprc.ff99SB
Log file: ./leap.log
Loading parameters: /opt/amber10/dat/leap/parm/parm99.dat
Reading title:
PARM99 for DNA,RNA,AA, organic molecules, TIP3P wat. Polariz.& LP
incl.02/04/99
Loading parameters: /opt/amber10/dat/leap/parm/frcmod.ff99SB
Reading force field modification type file (frcmod)
Reading title:
Modification/update of parm99.dat (Hornak & Simmerling)
Loading library: /opt/amber10/dat/leap/lib/all_nucleic94.lib
Loading library: /opt/amber10/dat/leap/lib/all_amino94.lib
Loading library: /opt/amber10/dat/leap/lib/all_aminoct94.lib
Loading library: /opt/amber10/dat/leap/lib/all_aminont94.lib
Loading library: /opt/amber10/dat/leap/lib/ions94.lib
Loading library: /opt/amber10/dat/leap/lib/solvents.lib
> source leaprc.gaff
----- Source: /opt/amber10/dat/leap/cmd/leaprc.gaff
----- Source of /opt/amber10/dat/leap/cmd/leaprc.gaff done
Log file: ./leap.log
Loading parameters: /opt/amber10/dat/leap/parm/gaff.dat
Reading title:
AMBER General Force Field for organic mol., add. info. at the end (June,
2003)
> loadamberparams frcmod.hemuni
Loading parameters: ./frcmod.hemuni
Reading force field modification type file (frcmod)
Reading title:
Force field modifcations for united atom heme, plus flexible water
WARNING: expected Improper Torsion PK>0 (0.000000)
Here is the Improper Torsion line in question:
X CC CC X 0 0.000 180.000 2.000
WARNING: expected Improper Torsion PK>0 (0.000000)
Here is the Improper Torsion line in question:
X CB NO X 0 0.000 180.000 2.000
WARNING: expected Improper Torsion PK>0 (0.000000)
Here is the Improper Torsion line in question:
X CB NP X 0 0.000 180.000 2.000
WARNING: expected Improper Torsion PK>0 (0.000000)
Here is the Improper Torsion line in question:
X CB CC X 0 0.000 180.000 2.000
>
please give me suggestions.
On Wed, Oct 13, 2010 at 10:52 PM, Bill Ross <ross.cgl.ucsf.edu> wrote:
> > Loading parameters: ./frcmod.hemuni
> > Reading force field modification type file (frcmod)
> > Reading title:
> > MASS
> > Unknown keyword: NP 14.01
>
> Evidently the frcmod is expected to have a title line, which is
> missing, so MASS is taken to be the title, and the mass lines
> are rejected for not being a keyword.
>
> Add a title line to the beginning of ./frcmod.hemuni
>
> Bill
>
>
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> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Nitu Bansal
M.S Pharm III Sem
Research Scholar
Center for Pharmacoinformatics
S.A.S Nagar NIPER Mohali (Chandigarh)
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Received on Wed Oct 13 2010 - 23:00:05 PDT
