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
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