AMBER Archive (2009)

Subject: RE: [AMBER] ERROR: Could not read coords from {filename}

From: ZhaoLei (jackyzhao010_at_hotmail.com)
Date: Mon Dec 28 2009 - 20:58:53 CST

Thank you for taking your time and Merry Christmas

Jakcy

> From: carlos.simmerling_at_gmail.com
> To: amber_at_ambermd.org
> Subject: Re: [AMBER] ERROR: Could not read coords from {filename}
> Date: Mon, 28 Dec 2009 21:04:27 -0500
>
> 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_at_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_at_biomaps.rutgers.edu
> >> To: amber_at_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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