hi all!
I got a fivefold coordinated heme in the protein I'm investigating, and
am subsequently using the parameter files is the /dat/contrib/heme folder:
source leaprc.ff99
loadamberparams /usr/local/amber8_64/dat/contrib/heme/frcmod.hemuni
loadamberprep /usr/local/amber8_64/dat/contrib/heme/heme_uni.in
prot = loadpdb "wt_ha.pdb"
...
Unfortunately I'm getting a bunch of errors after loading the parameters
and of course cannot save the modell. What am I doing wrong? It works
with the hemall files.
Thanks,
Simon
[sbecker.turn30 smd]$ tleap -s -f leap.inp
-I: Adding /usr/local/amber8_64/dat/leap/prep to search path.
-I: Adding /usr/local/amber8_64/dat/leap/lib to search path.
-I: Adding /usr/local/amber8_64/dat/leap/parm to search path.
-I: Adding /usr/local/amber8_64/dat/leap/cmd to search path.
-s: Ignoring startup file: leaprc
-f: Source leap.inp.
Welcome to LEaP!
Sourcing: ./leaper.inp
----- Source: /usr/local/amber8_64/dat/leap/cmd/leaprc.ff99
----- Source of /usr/local/amber8_64/dat/leap/cmd/leaprc.ff99 done
Log file: ./leap.log
Loading parameters: /usr/local/amber8_64/dat/leap/parm/parm99.dat
Loading library: /usr/local/amber8_64/dat/leap/lib/all_nucleic94.lib
Loading library: /usr/local/amber8_64/dat/leap/lib/all_amino94.lib
Loading library: /usr/local/amber8_64/dat/leap/lib/all_aminoct94.lib
Loading library: /usr/local/amber8_64/dat/leap/lib/all_aminont94.lib
Loading library: /usr/local/amber8_64/dat/leap/lib/ions94.lib
Loading library: /usr/local/amber8_64/dat/leap/lib/solvents.lib
Loading parameters: /usr/people/sbecker/frcmod.hemuni
Modified force field files must contain both a MASS and NONB entry, or
neither ############# here I guess? ####
Could not load parameter set.
-- no parameters loadedLoading Prep file: /usr/people/sbecker/heme_uni.in
Loading PDB file: ./wt_ha.pdb
Unknown residue: HEM number: 926 type: Terminal/last
..relaxing end constraints to try for a dbase match
-no luck
Creating new UNIT for residue: HEM sequence: 927
Created a new atom named: FE within residue: .R<HEM 927>
Created a new atom named: NA within residue: .R<HEM 927>
Created a new atom named: C1A within residue: .R<HEM 927>
Created a new atom named: C2A within residue: .R<HEM 927>
Created a new atom named: CAA within residue: .R<HEM 927>
Created a new atom named: CBA within residue: .R<HEM 927>
Created a new atom named: CGA within residue: .R<HEM 927>
Created a new atom named: O1A within residue: .R<HEM 927>
Created a new atom named: O2A within residue: .R<HEM 927>
Created a new atom named: C3A within residue: .R<HEM 927>
Created a new atom named: CMA within residue: .R<HEM 927>
--
Simon Becker
Dept. of Biology
Molecular Bioinformatics
Box M647
Universitaet Konstanz
D-78457 Konstanz
mail: simon.becker.uni-konstanz.de
Tel: 0049 7531 882900, Fax: 3183
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Received on Wed Nov 25 2009 - 08:30:02 PST
