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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--
-------------------------
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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Received on Wed Apr 15 2015 - 10:30:03 PDT
