[gmx-users] editconf -mead

[Mark Abraham]

marcos wrote:
> Hi,
> 
> editconf -mead writes a .pqr with a format "%10.5f%10.5f%10.5f" while it
> should be "%8.3f%8.3f%8.3f".
> Also the charges and radius are written in "%8.4f%8.4f" while the
> program pdb2pqr writes as "%8.4f%7.4f"
> 
> I changed line 167 of pdbio.c from:
> strcpy(pdbform,"%-6s%5u %-4.4s %3.3s %c%4d    %10.5f%10.5f%10.5f%8.4f%
> 8.4f\n");
> 
> to 
> 
> strcpy(pdbform,"%-6s%5u %-4.4s %3.3s %c%4d    %8.3%8.3f%8.3f%8.4f%7.4f
> \n");
> 
> and the .pqr is now ok. Will this change affect other programs?

I'm not aware that there is a standard for the PQR format. It's a hacked 
derivative of a PDB file. Some software that claims to read them 
probably constrains the format as for a PDB file, but others expect a 
free-form white-space-delimited format (e.g APBS, for which pdb2pqr 
prepares input). The two are not mutually consistent, so there will be 
problems.

It's straightforward to write a Perl script to convert from the above 
formats you describe in order to make some PQR-reading software happy. 
If someone writes one, add it to the contributions section of the 
GROMACS webpage.

Mark