Dear Dr. Jackie. J. Shen,
Thanks for your help, now I can solve my problem completely!
Best Regards
Rilei Yu
--- 09年4月21日，周二, Jackie. J. Shen <shj.ecust.163.com> 写道：
发件人: Jackie. J. Shen <shj.ecust.163.com>
主题: Re: Re: [AMBER] Backbone restraint
收件人: "AMBER Mailing List" <amber.ambermd.org>
日期: 2009年4月21日,周二,上午9:12
Hi Rilei,
You can just put the following line in your .in file:
ntr=1, restraint_wt=10.0, restraintmask=':
20-25.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.gmail.com> 写道：
>
>
>发件人: Carlos Simmerling <carlos.simmerling.gmail.com>
>主题: Re: [AMBER] Backbone restraint
>收件人: "AMBER Mailing List" <amber.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.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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Received on Wed May 20 2009 - 11:55:22 PDT
