Hi Arik,
Writing the PDB will most likely get rid of the box information I think.
Why not trajout individual restart files instead of pdbs? Is there a reason
you save a slew of PDB files? If you trajout directly to restart files I
think it should save the box info.
Your inpcrd file has lost its formatting in the email. Is there a line with
box information (3 numbers) at the very end? Make sure these are not
coordinates. You can check how many lines there should be just based on the
number of atoms in your system and given the fact that each atom has 3
coordinates.
Good luck!
Jason
On Fri, Aug 20, 2010 at 3:43 PM, arikcohen <arikcohen.ucla.edu> wrote:
> Hi Jason,
>
> Thanks a lot for tour ultrafast replay and above all your help.
>
> 1. The files that I'm using are the pdb which were taken via ptraj using
> the following command:
>
> trajin 1GTH_MD1.binpos 500 750 50
> trajout HG2.pdb pdb
> image familiar center
> go
>
> 2. The system is solvated with a box of TIP3P, 10 A around the protein.
>
> 3. The last couple of lines of my inpcrd file (taken again via ptraj)are
> as follows:
>
> 63.981 67.718 26.200 35.536 66.108 14.227 35.855 65.206
> 14.246 35.298
> 66.259 13.312 62.293 39.765 67.140 61.443 39.645 67.563
> 62.912 39.842
> 67.865 46.539 22.065 73.776 46.036 22.786 74.154 45.902
> 21.576 73.255
> 39.960 6.413 61.241 39.472 6.127 62.014 39.646 7.301 61.074
> 77.810 77.810 77.810
>
>
> Thanks a lot !!! again and all the best,
>
> Arik
> On 8/20/2010 4:31 AM, Jason Swails wrote:
> > Hello,
> >
> > Ptraj should not kill the box information without the keyword "nobox" at
> the
> > end of the trajout statement, to my understanding.
> >
> > What input file are you using? Is your system solvated? Should there be
> > box information? What do the last couple lines of your inpcrd file look
> > like?
> >
> > All the best,
> > Jason
> >
> > On Thu, Aug 19, 2010 at 8:35 PM, arikcohen<arikcohen.ucla.edu> wrote:
> >
> >> Dear Amber users,
> >>
> >> I would be most thankful for your help in the following problem: I'm
> >> trying to minimize snapshots(taken with ptraj) from a MD trajectory.
> >> However when doing so, I'm encountering the following error:
> >>
> >> 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
> >>
> >> Needless, to say that I have tried several things to resolve this issue
> >> among other things to manually entering the box dimensions into the
> >> inpcrd, or to get via ptraj the inpcrd files for the various snapshots,
> >> Non of which solved the problem.
> >> I would like to ask whether it is possible to create a pbc box with out
> >> solvating the system again ?.
> >>
> >> I thank you in advance for all your help.
> >>
> >> Arik
> >>
> >> _______________________________________________
> >> AMBER mailing list
> >> AMBER.ambermd.org
> >> http://lists.ambermd.org/mailman/listinfo/amber
> >>
> >
> >
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-4032
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Received on Fri Aug 20 2010 - 13:00:04 PDT
