[gmx-users] printing coordinates using template.c

Chandan Choudhury iitdckc at gmail.com
Tue Jun 8 17:52:22 CEST 2010


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.

Thanks

Chandan

--
Chandan kumar Choudhury
NCL, Pune
INDIA
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