Hi,
Amber 12 is a few years old at this point. I recommend upgrading to
AmberTools 14 and trying again - the 'unwrap' action in cpptraj was
vastly improved after AmberTools 12.
-Dan
On Wed, Apr 15, 2015 at 9:42 PM, pooja chahal <chahal.pooja.rs.gmail.com> wrote:
> 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)
>> >>
>> >> _______________________________________________
>> >> 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
>>
>>
>>
>> --
>> -------------------------
>> 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
>>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
--
-------------------------
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
Received on Thu Apr 16 2015 - 08:00:05 PDT
