Chandan Choudhury wrote:
Hello gmx users !!
I was trying to use template.c. There I printed out the coordinates of a
trajectory file using the printf statement as under:
printf("Coordinates at t=%8.3f : %8.5f %8.5f
%8.5f\n",fr.time,fr.x[n][XX],fr.x[n][YY],fr.x[n][ZZ]);
The output was
Reading frame 100 time 4400.000 Coordinates at t=4400.000 :
9.34053 4.26640 8.23887
This is the output of the 4400.000 th time or 100th frame of the first
Atom in the trr file.
Secondly, I dumped the 100th frame using tpbconv (of the same trajectory
as above) as:
trjconv -s *.tpr -f *.trr -dump 4400.00 -o frame100.pdb
The frame100.pdb reads as:
ATOM 1 N NGL A 1 93.405 42.664 82.389 1.00 0.00
ATOM 2 H1 NGL A 1 93.849 42.216 81.599 1.00 0.00
ATOM 3 H2 NGL A 1 93.914 43.464 82.737 1.00 0.00
ATOM 4 H3 NGL A 1 93.577 41.958 83.090 1.00 0.00
ATOM 5 CA NGL A 1 91.980 42.980 82.205 1.00 0.00
ATOM 6 HA NGL A 1 91.538 41.996 82.050 1.00 0.00
ATOM 7 CB NGL A 1 91.260 43.708 83.336 1.00 0.00
ATOM 8 HB1 NGL A 1 90.206 43.782 83.068 1.00 0.00
ATOM 9 HB2 NGL A 1 91.603 44.742 83.372 1.00 0.00
We can clearly see the difference in the coordinates of the 1st Atom
(ATOM 1 N).
That is the coordinates produced by the template are different than
those of trjconv's.
Can someone help me out to correctly printf the x, y z coordinate using
the template.c file.
Both are correct. Gromacs tools use nm units, and PDB files use Angstrom.
-Justin
Thanks
Chandan
--
Chandan kumar Choudhury
NCL, Pune
INDIA
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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