VMD-L Mailing List

From: Josh Vermaas (vermaas2_at_illinois.edu)
Date: Mon Aug 04 2014 - 08:58:10 CDT

Sure. The solvation plugin (Extensions, modeling) can do a waterbox
alone too.
-Josh

On 8/3/14, 9:41 PM, sunyeping wrote:
>
> Thank you Dr. Vermaas,
>
> But is there a way to generate a water box without protein in VMD?
>
> Yeping Sun
>
>
>
> ------------------------------------------------------------------
> 发件人：Josh Vermaas <vermaas2_at_illinois.edu>
> 发送时间：2014年8月3日(星期日) 20:25
> 收件人：孙业平 <sunyeping_at_aliyun.com>; vmd-l <vmd-l_at_ks.uiuc.edu>
> 主　题：Re: vmd-l: display water
>
> Use a surface representation (Quicksurf, MSMS, Surf), use one of the
> transparent representations, and color based on colorid, and use one
> of the blues. Its up to you to see which permutation of these elements
> you prefer.
> -Josh Vermaas
>
> On 08/03/2014 03:06 AM, sunyeping wrote:
>
> Dear all,
>
> Does some one know how to show water box as real water body? I
> mean make the water box look like real continous blue water, as
> the wate sphere around the ubiquitin
> <http://cn.bing.com/dict/clientsearch?mkt=zh-CN&setLang=zh&form=BDVEHC&q=%E6%B3%9B%E7%B4%A0#> molecule
> in cover page of the namd-turorial. Thank you!
>
> Yeping Sun
>
>
>