VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Sat Apr 20 2013 - 12:57:38 CDT

the pdb file format has very limited space to store all kinds of
information, thus you can't save coordinates in a pdb formatted file
that are too large in magnitude to fit that format. you need to use a
different file format.

axel.

On Fri, Apr 19, 2013 at 7:34 AM, Mohan maruthi sena
<maruthi.sena_at_gmail.com> wrote:
> Hi all,
> I have generated some random xyz coordinates as shown below :
> C -122.30999345 -226.62878095 14260.21711297
> C -193.01299627 170.48848092 14389.18215904
> C 165.21396622 197.5466634 14652.56309524
> C -253.07189228 47.69650083 14795.76483949
> C 138.40242423 -217.17529284 15009.15036761
> C -257.02414619 16.09121275 15159.71246634
> C 255.52035938 32.08870204 15386.64671586
> C -144.70465973 213.02793316 15431.3743127
> ......................................................................................................................................
> ......................................................................................................................................
> I have bunch of proteins , I want to place move geometrical center of
> these proteins to the above mentioned random points then, after moving all
> the centers of proteins to above points. I want to save them in one pdb
> file. When i do so , i get the following error,
> PDB WRITE ERROR: Position, occupancy, or b-factor (beta) for atom 0
> cannot be written in PDB format.
> By going through vmd mailing list I came to know that, if magnitude of
> coordinates is high the it will give these error. I want to save
> coordinates without transformation. If we can do by transformation , what
> kind of transformation need to be applied.
>
>
> **These random coordinates has a geometrical shape and some constraints
> between each point. These cannot be changed
>
> please suggest me a way,
>
>
> Thanks,
> Mohan
> 

-- 
Dr. Axel Kohlmeyer  akohlmey_at_gmail.com  http://goo.gl/1wk0
International Centre for Theoretical Physics, Trieste. Italy.