[gmx-developers] Coordinate scaling in pdbio.c

[Justin A. Lemkul]

Radhakrishna Bettadapura wrote:
> All,
> 
> I'm trying to figure out why a pdb input to pdb2gmx results in 
> coordinates that are scaled by a factor of 0.1. That is, if a line in 
> the PDB file reads
> 
> 
> ATOM      1  N   ALA B   3      -1.221  20.481  12.450  1.00 34.64       
>     N
> 
> then the corresponding line in the .gro file reads 
> 
> 
>  3ALA      N    1  -0.122   2.048   1.245
> 
> The culprit seems to be the following lines in pdbio.c:
> 
> static int read_atom(t_symtab *symtab,
>     char line[],int type,int natom,
>     t_atoms *atoms,rvec x[],int chainnum,gmx_bool bChange)
> {
> 
> // do stuff
> 
>  x[natom][XX]=strtod(xc,NULL)*0.1; /*all coordinates scaled by 0.1... why?*/
>   x[natom][YY]=strtod(yc,NULL)*0.1;
>   x[natom][ZZ]=strtod(zc,NULL)*0.1;
> 
> //do  more stuff
> 
> }
> 
> 
> There's also a line in the output function that multiplies all incoming 
> coordinates by 10 before writing it to output:
> 
> void write_pdbfile_indexed(FILE *out,const char *title,
>   t_atoms *atoms,rvec x[],
>   int ePBC,matrix box,char chainid,
>   int model_nr, atom_id nindex, atom_id index[],
>   gmx_conect conect, gmx_bool bTerSepChains)
> {
> 
> 
> //do stuff...
> 
> 
> fprintf(out,pdbform,pdbtp[type],(i+1)%100000,nm,resnm,ch,resnr,
>    (resic == '\0') ? ' ' : resic,
>    10*x[i][XX],10*x[i][YY],10*x[i][ZZ],occup,bfac,atoms->atom[i].elem);
>     
> // do more stuff...
> 
> }
> 
> 
> Can someone tell me why this coordinate scaling occurs?  And why the 
> scale factor is a single hard-coded number than, say, something that 
> depends on the input?
> 

PDB coordinates are in Angstrom, while .gro coordinates are in nm.  Hence the 
conversion factor of 0.1.

-Justin

-- 
========================================

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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