AMBER Archive (2009)

Subject: Re: [AMBER] Analysis of the solt-bridge

From: Rilei Yu (yulaomao1983_at_yahoo.com.cn)
Date: Mon Jun 29 2009 - 17:42:23 CDT

Dear Alessandro,
 
Thanks for your help! I thinks this way is very feasible!
 
Regards,

Rilei Yu

--- 2009-06-29 20:58:49， "Alessandro Nascimento" <al.s.nascimento_at_gmail.com>写道：

发件人: "Alessandro Nascimento" <al.s.nascimento_at_gmail.com>
主题: Re: [AMBER] Analysis of the solt-bridge
收件人: "AMBER Mailing List" <amber_at_ambermd.org>
日期: 2009-06-29 20:58:49

Hi Rilei Yu

You can try hbond facility in ptraj, which is very helpful (see the
documentation for ptraj in amber manual)
Other than that, you can try the salt bridge plugin in vmd
(http://www.ks.uiuc.edu/Research/vmd/plugins/saltbr)

Hope that helps,

--Alessandro

On Sun, Jun 28, 2009 at 7:24 PM, Rilei Yu<yulaomao1983_at_yahoo.com.cn> wrote:
> Dear amber users,
>
> Can anyone tell me weather there are some scripts for me to analysis the solt-bridge between the receptor and the ligand from the MD traj. file?  Or is there any other software that can be used to analysis the solt-brige in one snapshot?
>
> Best Regards,
>
> Rilei Yu
>
>
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-- 
[ ]s

--alessandro

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