Re: [AMBER] How can I fix two ends of DNA?

From: Jason Swails <jason.swails.gmail.com>
Date: Tue, 10 Apr 2012 00:40:52 -0400

Ah, well, see if it works then.

I thought the behavior I described was a limitation in the code. If I am right, you should see some vague error about "rfree" expecting more integers or something (and we should make a note about it on the website or something). If I am wrong it should work fine.

Good luck!
Jason

PS -- another reason I thought what I thought was because if "single" residues could be specified, then what does

RES 2 8

mean? Is it residues 2 to 8? Or is it residues 2 and 8? Forcing the latter (just 2 and 8) to be

RES 2 2 8 8

removes the ambiguity. Just my opinion.

--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
On Apr 9, 2012, at 7:08 PM, mehdi bagherpoor <ms.nightsky.gmail.com> wrote:
> On Mon, Apr 9, 2012 at 7:38 AM, Jason Swails <jason.swails.gmail.com> wrote:
> 
>> Dave's advice is good, I just had one minor addition.
>> 
>> On Sun, Apr 8, 2012 at 6:20 AM, mehdi bagherpoor <ms.nightsky.gmail.com
>>> wrote:
>>> 
>>> /
>>> Hold the DNA fixed
>>> 10
>>> RES 1
>>> 
>> 
>> This group input is wrong.  You need to specify an atom range.  If you wish
>> to select a single atom, select it like this:
>> 
>> RES 1 1
>> 
>> Hold the DNA fixed
>>> 10
>>> RES 34
>>> 
>> 
>> Here, too, this line needs to be
>> 
>> RES 34 34
>> 
>> HTH,
>> Jason
>> 
> 
> 
> 
> Hello Jason
> Thanks
> 
> but in Amber10 Manual at page 267 has written for sample:
> 
> Input 1:
>  Title one
>  RES 1 5
>  END
>  Title two
>  RES 6
>  END
>  END
> 
> 
>> 
>> --
>> Jason M. Swails
>> Quantum Theory Project,
>> University of Florida
>> Ph.D. Candidate
>> 352-392-4032
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>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>> 
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Received on Mon Apr 09 2012 - 22:00:05 PDT