Hi,
I am using cpptraj (AMBER 12 version ). The input file for cpptraj that I
am using is as follow:
trajin traj1
trajin traj2
unwrap
trajout x.out pdb multi nobox
I am getting following error:
ACTIONS: Initializing 1 actions:
0: [unwrap]
PTRAJ ACTION: [unwrap]
BEGIN TRAJECTORY PROCESSING:
.....................................................
PARM [abc.parm7]: Setting up 1 actions.
0: [unwrap]
Mask [*] represents 23012 atoms
UNWRAP
The atoms in the calculation follow: * (All atoms are selected)
----- [abc_prod1.mdcrd] (1-1000, 1) -----
0% Warning: Action [unwrap] failed, frame 0.
On Wed, Apr 15, 2015 at 10:43 PM, Daniel Roe <daniel.r.roe.gmail.com> wrote:
> Hi,
>
> On Wed, Apr 15, 2015 at 6:25 AM, pooja chahal <chahal.pooja.rs.gmail.com>
> wrote:
> > Thanks for the reply. I have tried cpptraj following your suggestion but
> I
> > am unable to unwrap the trajectory using cpptraj. I have no prior
> > experience of using cpptraj. Also asterisks are not observed in the
> > original ASCII trajectory file. As I have mentioned earlier, I have used
> > iwrap=1 during my production run.
>
> Could you provide some more detail on how you were unable to unwrap
> with cpptraj? Does it not recognize the command? Does it give an error
> message? What version of cpptraj have you tried?
>
> -Dan
>
> >
> > On Tue, Apr 14, 2015 at 7:36 PM, Daniel Roe <daniel.r.roe.gmail.com>
> wrote:
> >
> >> Hi,
> >>
> >> On Mon, Apr 13, 2015 at 10:42 PM, pooja chahal
> >> <chahal.pooja.rs.gmail.com> wrote:
> >> > Also one more thing that I am observing is that while generating .pdb
> >> files
> >> > using ptraj with unwrap command, some of atoms attains a very high
> >> negative
> >> > value (< -1000) for coordinates. For these coordinates "********"
> appears
> >> > in the .pdb file instead of real coordinates. However, this is not the
> >> only
> >>
> >> This seems odd to me. The multiple asterisks is something that fortran
> >> code does for numerical overflow, not C/C++ code (to my knowledge).
> >> You shouldn't be getting asterisks in your PDB files if you're
> >> creating them with ptraj. Do you get the same behavior with cpptraj?
> >>
> >> If on the other hand you mean you see asterisks in the original ASCII
> >> trajectory file then your coordinates overflowed during your
> >> simulation and there is no way to recover them. For this reason it is
> >> recommended that during simulations you use 'iwrap=1' to enable
> >> imaging, 'ioutfm=1' to write NetCDF trajectories, and 'ntxo=2' to
> >> write NetCDF restart files; the NetCDF file format is not nearly as
> >> susceptible to issues as the ASCII format.
> >>
> >> Hope this helps,
> >>
> >> -Dan
> >>
> >> --
> >> -------------------------
> >> Daniel R. Roe, PhD
> >> Department of Medicinal Chemistry
> >> University of Utah
> >> 30 South 2000 East, Room 307
> >> Salt Lake City, UT 84112-5820
> >> http://home.chpc.utah.edu/~cheatham/
> >> (801) 587-9652
> >> (801) 585-6208 (Fax)
> >>
> >> _______________________________________________
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> >> http://lists.ambermd.org/mailman/listinfo/amber
> >>
> > _______________________________________________
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>
>
>
> --
> -------------------------
> Daniel R. Roe, PhD
> Department of Medicinal Chemistry
> University of Utah
> 30 South 2000 East, Room 307
> Salt Lake City, UT 84112-5820
> http://home.chpc.utah.edu/~cheatham/
> (801) 587-9652
> (801) 585-6208 (Fax)
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Wed Apr 15 2015 - 21:00:02 PDT
