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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Received on Mon Dec 28 2009 - 18:00:02 PST
