Dear Amber community members,
I am trying to prepare amber input files for Cytochrome P450. i am using
hemeuni files from
http://www.pharmacy.manchester.ac.uk/bryce/amber
in this it showed the problem of masses i add them as
MASS
NP 14.01
NO 14.01
CY 13.0
CX 14.0
CD 13.0
FE 55.85
LC 12.01
LO 16.00
HW 01.00
CL 35.45
these steps i am following
[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 BHF.frcmod
Loading parameters: ./BHF.frcmod
Reading force field modification type file (frcmod)
Reading title:
remark goes here
> loadamberprep BHF.prepin
Loading Prep file: ./BHF.prepin
> loadamberparams frcmod.hemuni
Loading parameters: ./frcmod.hemuni
Reading force field modification type file (frcmod)
Reading title:
MASS
Unknown keyword: NP 14.01
in parameter file.
Unknown keyword: NO 14.01
in parameter file.
Unknown keyword: CY 13.0
in parameter file.
Unknown keyword: CX 14.0
in parameter file.
Unknown keyword: CD 13.0
in parameter file.
Unknown keyword: FE 55.85
in parameter file.
Unknown keyword: LC 12.01
in parameter file.
Unknown keyword: LO 16.00
in parameter file.
Unknown keyword: HW 01.00
in parameter file.
Unknown keyword: CL 35.45
in parameter file.
!FATAL ERROR----------------------------------------
!FATAL: In file [varArray.c], line 106
!FATAL: Message: PVarArrayIndex: VARARRAY is NULL!
!ABORTING.
please give me suggestions.
--
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 - 10:30:04 PDT
