linux下生成1M全FF文件,在linux系统终端里用amber的tleap生成top和crd文件的基本程序...

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

.

.

.

.

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

.

.

.

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.