[gmx-users] Atom definition in atomname2type.n2t file

[Adnan Shahriar]

Hi,

I like to use x2top command to generate a primitive topology file for
Graphene Oxide, where I have defined new Atoms with new Types. This
requires a file, *atomname2type.n2t *that contains data like this,

C    opls_157    -0.18 12.011 4    H 0.108   H 0.108   H 0.108   C 0.150
C    opls_158    -0.12  12.011 4    H 0.108   H 0.108   C 0.150   C 0.150
C    opls_157    0.145  12.011 4    H 0.108   O 0.141   H 0.108   C 0.150
C    opls_157    0.145  12.011 4    H 0.108   H 0.108   O 0.108   C 0.150
....

I have modified it like this,

CAg   CAg    0.00      12.011  3    CAg 0.141   CAg 0.141   CAg 0.141
CTal   CTal    0.00      12.011  3    CAg 0.141   CAg 0.141   CAg 0.141
CTal   CTal    0.00      12.011  3    CAg 0.141   CToh 0.141   CAg 0.141
CTal   CTal    0.00      12.011  3    CAg 0.141   CAe 0.141   CAg 0.141
CTal   CTal    0.00      12.011  3    CAg 0.141   CToh 0.141   CAe 0.141
CTal   CTal    0.00      12.011  3    CTal 0.141   CAg 0.141   CAg 0.141
.......

But this is too tiring as it requires a lot combination. So what I want to
do is assign CAg, CTal as C and make it very simple like this,

CAg   CAg    0.00      12.011  3    C 0.141   C 0.141   C 0.141
CTal   CTal    0.00      12.011  3    C 0.141   C 0.141   C 0.141
....

So, how can I do that?

Thanks in advance.

Adnan
undefined.shahriar at gmail.com