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

majid hasan pu_majidhasan at yahoo.com
Tue Apr 19 19:17:24 CEST 2011

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: 

    1TUB     CA    1   0.392   0.000   0.000
so I opened oplsaa's .n2t file, and replaced all the entries with these three 
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. 

Any help is much appreciated.

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