[gmx-users] atomname2type.n2t file for CNT in amber99

[Justin A. Lemkul]

majid hasan wrote:
> Dear All,
> 
> In an attempt to create CNT topology with g_x2top and amber99, I was 
> getting this error: no or incorrect atomname2type.n2t file found. So I 
> tried to create a atomname2type.n2t file for CNT in Amber99. My 
> coordinate file is of this form:
> UNNAMED
>   400
>     1TUB     CA    1   0.392   0.000   0.000
>  
> so I opened oplsaa's .n2t file, and replaced all the entries with these 
> three lines:
> CA           C     0      12.011  3    C 0.142   C 0.142   C 0.142
> CA         CA    0      12.011  2    C 0.142   C 0.142
> CA         CB    0      12.011  1    C 0.142  
> 
> C, CA, CB are all listed in atomtypes.atp file in Amber as:
> C                 12.01000    ; sp2 C carbonyl group
> CA                12.01000    ; sp2 C pure aromatic (benzene)
> CB                12.01000    ; sp2 aromatic C, 5&6 membered ring junction
> 
> 
> But when I run the g_x2top, I still get the same error.
> 

And where is this .n2t file located?  It needs to be in the amber99.ff directory 
to actually work, and you need to provide this force field's name in your 
g_x2top command, which unfortunately you have not posted.

-Justin

> Any help is much appreciated.
> 
> Thanks,
> Majid
> 

-- 
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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