AMBER Archive (2009)

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

From: Alessandro Nascimento (al.s.nascimento_at_gmail.com)
Date: Mon Jun 29 2009 - 07:58:49 CDT

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
>
>
> ___________________________________________________________
> 好玩贺卡等你发，邮箱贺卡全新上线！
> http://card.mail.cn.yahoo.com/
> _______________________________________________
> AMBER mailing list
> AMBER_at_ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
> 

-- 
[ ]s

--alessandro

_______________________________________________
AMBER mailing list
AMBER_at_ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber