Re: On naming rules in force-field parameter files?

From: Ramya Gamini (ramyabhargavi_at_gmail.com)
Date: Mon Aug 10 2009 - 09:07:12 CDT

Hi !
Yes, you can use wildcards. However, in CHARMM, the wildcard notation to be
used is not an asterik '*', but, the letter X (note the Caps).

Also, if you have all of them same and only of them (for eg: Au_2 Au_3 Au_5
to be different), then you would mention it as the following:

For instance:

Au_X Au_X Au_X 2.5 180
Au_2 Au_3 Au_5 2.5 120

In effect you would see, Au_2 Au_3 Au_5 2.5 120.

However, if you have the lines interchanged,
Au_2 Au_3 Au_5 2.5 120
Au_X Au_X Au_X 2.5 180

then, Au_2 Au_3 Au_5 will be set to :
Au_2 Au_3 Au_5 2.5 180

hope it helps.
Ramya

On Sun, Aug 9, 2009 at 8:12 PM, He Yuhui <yuhuihe_at_ime.pku.edu.cn> wrote:

> Dear all,
>
> I am doing some research on DNA and gold electrode systems. When
> generating psf files, I set 12 types of Au atoms according to their bond
> numbers. That is, Au_1, Au_2, ..., Au_12.
>
> However, it will be very tedious when I modify the CHARMM force-field
> parameter files, e.g., I have to write about 12*11*10/(3*2) lines on
> angles:
> Au_1 Au_2 Au_3 ... ...
> Au_1 Au_2 Au_4 ... ...
> ...
>
> So I wonder whether I can write just one line with an asterisk
> wildcard:
> Au_* Au_* Au_* ... ...
>
> Thanks and Regards!
>
> Yuhui
>
> ---
> Dr. Yuhui He(何毓辉)
> Institute of Microelectronics, Chinese Academy of Sciences
> Beijing 100029, China
>
>
>
>
>
>
>

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