AMBER Archive (2009)

Subject: Re: Re: [AMBER] Backbone restraint

From: Jackie. J. Shen (shj.ecust_at_163.com)
Date: Mon Apr 20 2009 - 20:12:13 CDT

Hi Rilei,

You can just put the following line in your .in file:

ntr=1, restraint_wt=10.0, restraintmask=':20-25_at_CA',

J
2009-04-21

-----------------------Original-------------------------
>From：Rilei Yu
>Sent：2009-04-18 11:29:54
>To：AMBER Mailing List
>Cc：
>Subject：Re: [AMBER] Backbone restraint

>>
>Thanks for your suggestion! But maybe I have missed it! I found the example that carry out MD on the restraint while residues rather than backbone.
>For example it uses RES 20 25 to restraint all the atoms in the residues between 20_25. Now, I want to restraint the "CA backbone"
>?
>I hope you can give me more specific details. And I am really appreciated for your help!
>?
>Best wishes,
>
>Rilei Yu
>
>--- 09年4月18日，周六, Carlos Simmerling <carlos.simmerling_at_gmail.com> 写道：
>
>
>发件人: Carlos Simmerling <carlos.simmerling_at_gmail.com>
>主题: Re: [AMBER] Backbone restraint
>收件人: "AMBER Mailing List" <amber_at_ambermd.org>
>日期: 2009年4月18日,周六,上午10:35
>
>
>it's pretty well documented in the manual and examples in the test
>cases- look at the positional restraints, set by ntr=1. it will do
>exactly what you need.
>
>
>On Fri, Apr 17, 2009 at 10:30 PM, Rilei Yu <yulaomao1983_at_yahoo.com.cn> wrote:
>>
>> Dear AMBER users,
>>
>> I want to perform MD on protein-ligand complex to consider the flexibility of the side chains in the binding pocket. So I want to restraint the backbone of the receptor, while the side chains are not restrainted. Can anyone tell me some script that can carry out this function?
>>
>> Best Regards,
>> Rilei Yu
>>
>>
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