[gmx-users] about CNT simulation

bo yang suriayang at gmail.com
Thu May 31 18:27:04 CEST 2007

Dear gromacs users,

Thank you for your answering my previous questions.
Here, I am in trouble again.
I continue the simulation of DNA, carbon nanatube and water.
I changed the names of atoms in cnt.pdb according to the names in
When I performed the energy minimization, the result I get is :

"Fatal error:
Invalid order for directive defaults, file ""ffamber99.itp"", line 4".

I checked back ffamber99.itp, the whole file is simple :
"#define _FF_AMBER
 #define _FF_AMBER99

[ defaults ]
; nbfunc        comb-rule       gen-pairs       fudgeLJ fudgeQQ
  1             2               yes             0.5     0.8333

#include "ffamber99nb.itp"
#include "ffamber99bon.itp"

Can you give me some suggestions and help me out?
Also, I have a question regarding the residue names in amber99.
I guess that I may also need to change the residue of CNT(carbon nanotube)
according to the residue names used in ffamber99.
Do you think that it is necessary? And, how can I do it?

Thank you so much!

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