Re: [AMBER] cpptraj/parmbox

From: Daniel Roe <daniel.r.roe.gmail.com>
Date: Fri, 26 Sep 2014 11:21:42 -0600

Hi,

You've come across a corner case. The problem is that since the
trajectory only contains box lengths (no angles), cpptraj by default
checks the topology to determine what kind of box is present. However,
since you are presumably using your PDB file as your topology (which
has no box info), cpptraj doesn't know what kind of box it is. In the
end the coordinates are read in fine, but the box information is not
used because cpptraj doesn't assume the box is orthogonal.

The 'parmbox' command can help, but since you only gave it lengths
(not angles) it still has no idea what the box type is. Add 'alpha 90
beta 90 gamma 90' to the 'parmbox' command to set an orthogonal box.

Hope this helps,

-Dan


On Fri, Sep 26, 2014 at 8:19 AM, amirhossein taghavi
<amirhosseintaghavi240.yahoo.com> wrote:
> Hi,
>
> The original trajectory file is the output of my MC code for GC DNA modeling
> in the xyz format.I have two scripts which produce pdb and trj files which
> based on that cpptraj analysis is done.
>
> This is a sample of cpptraj output:
>
> Reading '1.xyz.pdb' as PDB File
> 1.xyz.pdb: determining bond info from distances.
> Warning: 1.xyz.pdb: Determining default bond distances from element types.
> INPUT: Reading Input from STDIN
> [parmbox x 136.12 y 136.12 z 136.12]
> [trajin 1.xyz.trj]
> Reading '1.xyz.trj' as Amber Trajectory
> [distance .82 @82 out distBB_41.dat geom noimage]
> DISTANCE: .82 to @82, non-imaged, geometric center.
>
> I have attached the original trajectory file and trj,pdb files hope that it
> helps.if the scripts that are used to get pdb and trj files are also needed
> please let me know.
>
> Thanks in Forward
> Amir
>
>
>
>
> On Friday, September 26, 2014 4:00 PM, Daniel Roe <daniel.r.roe.gmail.com>
> wrote:
>
>
> Hi,
>
> We need much more information on how the original trajectory was
> generated, as well as the full cpptraj output to even begin to
> diagnose this problem.
>
> -Dan
>
> On Fri, Sep 26, 2014 at 1:13 AM, amirhossein taghavi
> <amirhosseintaghavi240.yahoo.com> wrote:
>> Hello everyone,
>>
>> My rpoblem is not directly related to MD but as I use Amber cpptraj to
>> analyze my data, I wondered may some one could have some help!!
>>
>> I have a CG model of DNA in xyz format and I am using cpptraj to do some
>> measurements on bonds,angles and dihedrals.The problem is, for example, when
>> I calculate the base interdistances with piece of a script I have, in some
>> frames the distance is calculated with the image of particle at the end of
>> the box, like say my box is 136A. so if the usual BB distance is between
>> 5-7A is some frames it jumps tp 136.
>> I have added parmbox information to the script but the problem still
>> exists.
>> any help or suggestion is highly appreciated.
>>
>> Thanks in Forward
>
>> _______________________________________________
>> 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)
>



-- 
-------------------------
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 Fri Sep 26 2014 - 10:30:02 PDT
Custom Search