Read the archives about the ptraj image command. It will do what you
need an has been extensively disussed in the past.
On Dec 28, 2009, at 8:34 PM, ZhaoLei <jackyzhao010.hotmail.com> wrote:
>
> Thank you for your immediately reply. According to your suggestion,
> I have resimulated the protein complex from 35ns (the most recent
> rst file). During the simulation process, I viewed the simulated
> structure using the rst file generated during the process and the
> prmtop file. I found that the protein complex was not in the center
> of the TIP3P water box, and part of the protein complex was out of
> the water box.
>
> I'm so sorry to borther you again. I'm a beginner of Amber. So I
> have resimulated from the start of the whole simulation procedure.
> Additionally, even I have added the "iwrap=1" in the end of the
> heating the whole complex. The shifting out of the water box is
> still happened. So I have adding "iwrap=1" in the begin of the
> heating process. Do you think adding "iwrap=1" during heating the
> whole complex is appropriate way?
>
>
> Jacky
>
>> Date: Mon, 28 Dec 2009 09:57:11 -0500
>> From: case.biomaps.rutgers.edu
>> To: amber.ambermd.org
>> Subject: Re: [AMBER] ERROR: Could not read coords from {filename}
>>
>> On Mon, Dec 28, 2009, ZhaoLei wrote:
>>>
>>>
>>> Would you mind to give us some suggestions about the criterion to
>>> choose the last good restart file ? According to your suggestion, we
>>> do not need to restart the simulation from the beginning of the
>>> whole
>>> simulation procedure ?
>>
>> The last "good" file is the most recent one that does not have
>> "****" in it.
>>
>>>
>>> Just as you have mentioned, during the long-term simulation we would
>>> better turn on the binary restrart file (using "ioutfm" command)?
>>> would
>>> mind to give us some more detail explaination ?
>>
>> It is my understanding that binary restart files have been disabled
>> in Amber
>> 10, so that this is not an option. The "ioutfm" variable refers to
>> the
>> trajectory files, not to the restart files; the manual is a bit
>> confusing
>> here.
>>
>> ...dac
>>
>>
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>
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Received on Mon Dec 28 2009 - 18:30:03 PST
