[gmx-users] about CNT simulation

[Mark Abraham]

bo yang wrote:
> 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 
> ffamberXX.itp.
> 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?

First, I read the error message and realise that grompp thinks the 
"defaults" directive is in an invalid order. Then, I head to the manual, 
chapter five, to find out about this directive and the order it should 
be in. Here's your big hint... there can only be one of them in your .top.

> 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?

We can't tell from what you've said so far. Lots of reading of chapter 5 
is in order here :-)

Mark