[gmx-users] Re: printing coordinates using template.c

[Vitaly Chaban]

Chandan -

Hmm... What's the problem? template.c gives the numbers in NANOMETERS
while PDB file contains them in ANGSTROMS.

To my knowledge, nowadays gromacs people use XDRFILE library to work
with trajectories -
http://www.gromacs.org/index.php?title=Download_%26_Installation

-- 
Dr. Vitaly Chaban



> 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  8.23887e
> 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