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

[Dallas Warren]

Since the .n2t file has a set format, easiest way is to write yourself
a script that will generate the required combinations and print out
the result for you.
Catch ya,

Dr. Dallas Warren
Drug Delivery, Disposition and Dynamics
Monash Institute of Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3052
dallas.warren at monash.edu
---------------------------------
When the only tool you own is a hammer, every problem begins to resemble a nail.


On 21 October 2017 at 04:55, Adnan Shahriar
<undefined.shahriar at gmail.com> wrote:
> 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
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