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panhuairen

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[½»Á÷] ¡¾ÇóÖú¡¿Amber µÄXleap Óöµ½µÄÎÊÌâ

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Here are commands:
________________________________________________________________________
>[root@localhost amber_tutorial]# $AMBERHOME/exe/tleap -s -f $AMBERHOME/dat/leap/cmd/leaprc.rna.ff99
-I: Adding /usr/local/amber9/dat/leap/prep to search path.
-I: Adding /usr/local/amber9/dat/leap/lib to search path.
-I: Adding /usr/local/amber9/dat/leap/parm to search path.
-I: Adding /usr/local/amber9/dat/leap/cmd to search path.
-s: Ignoring startup file: leaprc
-f: Source /usr/local/amber9/dat/leap/cmd/leaprc.rna.ff99.

Welcome to LEaP!
Sourcing: /usr/local/amber9/dat/leap/cmd/leaprc.rna.ff99
Log file: ./leap.log
Loading parameters: /usr/local/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: /usr/local/amber9/dat/leap/lib/all_nucleic94.lib
Loading library: /usr/local/amber9/dat/leap/lib/all_amino94.lib
Loading library: /usr/local/amber9/dat/leap/lib/all_aminoct94.lib
Loading library: /usr/local/amber9/dat/leap/lib/all_aminont94.lib
Loading library: /usr/local/amber9/dat/leap/lib/ions94.lib
Loading library: /usr/local/amber9/dat/leap/lib/solvents.lib
> x = loadpdb "final_bf_dm.pdb"
Loading PDB file: ./final_bf_dm.pdb
Created a new atom named: P within residue: .R
Created a new atom named: O1P within residue: .R
Created a new atom named: O2P within residue: .R
Created a new atom named: H2* within residue: .R
Created a new atom named: HO2* within residue: .R
................................
.............
.......
Created a new atom named: HO2* within residue: .R
Created a new atom named: H2* within residue: .R
Created a new atom named: HO2* within residue: .R
Created a new atom named: H2* within residue: .R
Created a new atom named: HO2* within residue: .R
Created a new atom named: H2* within residue: .R
Created a new atom named: HO2* within residue: .R
Created a new atom named: H2* within residue: .R
Created a new atom named: HO2* within residue: .R
  total atoms in file: 1944
  Leap added 194 missing atoms according to residue templates:
       70 Heavy
       124 H / lone pairs
  The file contained 195 atoms not in residue templates
>
___________________________________________________________________
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[ Last edited by zzgyb on 2008-7-20 at 18:59 ]
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