this depends on which version of amber you are using, which you did
not say. in amber10, you can use restraintmask to specify atoms. the
manual gives examples, and you can also find many examples using the
serach on the amber web page- look for "restraintmask"
On Fri, Apr 17, 2009 at 11:29 PM, Rilei Yu <yulaomao1983.yahoo.com.cn> wrote:
> 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 - 11:35:32 PDT
