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

From: Schreiner Eduard (eschrein_at_ks.uiuc.edu)
Date: Sun Aug 09 2009 - 20:27:17 CDT

if the parameters are same, why do you need 12 types for Au atoms?

apart from that, I'm not aware of wild cards usage (apart in dehedrals
and impropers)
  in charmm or amber force fileds,
but maybe somebody else would like to point us to another case.

eddi

On Aug 9, 2009, at 8:12 PM, He Yuhui 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
>
>
>
>
>

=====================================================
Eduard Schreiner
Theoretical and Computational Biophysics Group
NIH Resource for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave., Urbana, IL 61801
Phone: 217-244-4361
Fax: 217-244-6078
http://www.ks.uiuc.edu/~eschrein/
=============================================

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