1# 北极的企鹅 .你好,下面是我制作碳纳米管top和crd文件的过程和出现的错误,麻烦你帮我看看啊。谢谢
[email=wsh@wsh-K42JE:~$]
wsh@wsh-K42JE:~$
[/email] tleap -s -f leaprc.ff99SBildn
-I: Adding /home/wsh/amber12/dat/leap/prep to search path.
-I: Adding /home/wsh/amber12/dat/leap/lib to search path.
-I: Adding /home/wsh/amber12/dat/leap/parm to search path.
-I: Adding /home/wsh/amber12/dat/leap/cmd to search path.
-s: Ignoring startup file: leaprc
-f: Source leaprc.ff99SBildn.
Welcome to LEaP!
Sourcing: /home/wsh/amber12/dat/leap/cmd/leaprc.ff99SBildn
Log file: ./leap.log
Loading parameters: /home/wsh/amber12/dat/leap/parm/parm99.dat
Reading title:
PARM99 for DNA,RNA,AA, organic molecules, TIP3P wat. Polariz.& LP incl.02/04/99
Loading parameters: /home/wsh/amber12/dat/leap/parm/frcmod.ff99SBildn
Reading force field modification type file (frcmod)
Reading title:
Modification/update of parm99.dat (Hornak & Simmerling) ILDN corrections
Loading library: /home/wsh/amber12/dat/leap/lib/all_nucleic94.lib
Loading library: /home/wsh/amber12/dat/leap/lib/all_amino94ildn.lib
Loading library: /home/wsh/amber12/dat/leap/lib/all_aminoct94ildn.lib
Loading library: /home/wsh/amber12/dat/leap/lib/all_aminont94ildn.lib
Loading library: /home/wsh/amber12/dat/leap/lib/ions94.lib
Loading library: /home/wsh/amber12/dat/leap/lib/solvents.lib
> A=loadpdb CNT.pdb
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.
.
.
Created a new atom named: C309 within residue: .R
Created a new atom named: C918 within residue: .R
Created a new atom named: C728 within residue: .R
Created a new atom named: C299 within residue: .R
Created a new atom named: C109 within residue: .R
Created a new atom named: C399 within residue: .R
Created a new atom named: C289 within residue: .R
Created a new atom named: C279 within residue: .R
Created a new atom named: C089 within residue: .R
Created a new atom named: C389 within residue: .R
Created a new atom named: C269 within residue: .R
total atoms in file: 940
The file contained 940 atoms not in residue templates
> saveamberparm A CNT.prmtop CNT.inpcrd
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.
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FATAL:Atom .R.A does not have a type.
FATAL:Atom .R.A does not have a type.
FATAL:Atom .R.A does not have a type.
FATAL:Atom .R.A does not have a type.
FATAL:Atom .R.A does not have a type.
FATAL:Atom .R.A does not have a type.
FATAL:Atom .R.A does not have a type.
FATAL:Atom .R.A does not have a type.
FATAL:Atom .R.A does not have a type.
FATAL:Atom .R.A does not have a type.
FATAL:Atom .R.A does not have a type.
FATAL:Atom .R.A does not have a type.
FATAL:Atom .R.A does not have a type.
Failed to generate parameters
Parameter file was not saved.