Nevermind, that was for periodic simulation. For non-periodic system, page 64 of the manual has more relevance. I apologize for the confusion.
--Farid
________________________________________
From: Ismail, Mohd F. [farid.ou.edu]
Sent: Thursday, August 11, 2011 1:23 PM
To: AMBER Mailing List
Subject: Re: [AMBER] Inpcrd file problem
After solvating it, before saving the parameter, did you do "set moleculename box value"?
--Farid
________________________________________
From: David Cantu [cantudav.amber.gmail.com]
Sent: Thursday, August 11, 2011 12:27 PM
To: AMBER Mailing List
Subject: Re: [AMBER] Inpcrd file problem
Hi,
I made the inpcrd on Xleap, after solvating a protein.
David
On Thu, Aug 11, 2011 at 11:58 AM, Daniel Roe <daniel.r.roe.gmail.com> wrote:
> Hi,
>
> Ptraj will say something like:
>
> ...
> INPUT COORDINATE FILES
> File (step9.rst7) is an AMBER restart file with box and velocity
> information
> ...
>
> If ptraj indicates the restart file does not have box information and
> it is supposed to then there may be a problem with your restart.
>
> -Dan
>
> On Thu, Aug 11, 2011 at 11:57 AM, David Cantu <cantudav.amber.gmail.com>
> wrote:
> > This is supposed to have box coordinates.
> >
> > We made the inpcrd file on Xleap, and its the first time this error came
> up.
> >
> > Ptraj can read the inpcrd. What output should I look for in ptraj? We
> have
> > not been able to run any minimization or MD.
> >
> > Thanks,
> >
> > David
> >
> > On Thu, Aug 11, 2011 at 10:31 AM, Daniel Roe <daniel.r.roe.gmail.com>
> wrote:
> >
> >> Hi,
> >>
> >> Are you certain your inpcrd file has box coordinates? You can check
> >> this by reading it into ptraj or cpptraj and checking the output.
> >> Alternatively, if the inpcrd file is not supposed to have box
> >> coordinates ntb should be 0.
> >>
> >> -Dan
> >>
> >> On Thu, Aug 11, 2011 at 10:53 AM, David Cantu <cantudav.amber.gmail.com
> >
> >> wrote:
> >> > Dear Amber Users/Developers:
> >> >
> >> > We are getting the following error when trying to run a minimization:
> >> >
> >> > | Flags:
> >> > MPI
> >> > getting new box info from bottom of inpcrd
> >> > | INFO: Old style inpcrd file read
> >> > | peek_ewald_inpcrd: Box info not found in inpcrd
> >> >
> >> > This appears at the bottom of the .out file, which is attached if you
> >> want
> >> > to see the whole file. The inpcrd file was too big to post in the
> forum
> >> > without approval. I can send the inpcrd file to whoever owuld like to
> >> look
> >> > at it.
> >> >
> >> > Any ideas why this error comes up?
> >> >
> >> > Thank you,
> >> >
> >> > David
> >> >
> >> > _______________________________________________
> >> > AMBER mailing list
> >> > AMBER.ambermd.org
> >> > http://lists.ambermd.org/mailman/listinfo/amber
> >> >
> >> >
> >>
> >> _______________________________________________
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> >> http://lists.ambermd.org/mailman/listinfo/amber
> >>
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> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
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Received on Thu Aug 11 2011 - 12:30:02 PDT
