Should non ATOM or HETATM lines be ignored in pqr2xml

[Lane Votapka]

Hi Gary,

I've generated some PQR files using automated software (parmed), and by default, it writes a CRYST line at the beginning of the PQR. For example:

CRYST1   75.083   75.083   75.083 109.47 109.47 109.47
HETATM    1  C12  MOL     1     33.525  41.350  37.722  -0.6005   1.7000
HETATM    2  H7   MOL     1     32.548  41.184  38.194   0.1131   1.2000

...

It's not much trouble to modify the files by hand, and there might be a way that I can find how to tell parmed not to write the CRYST line, but would it be possible to change pqr2xml to ignore all non-(ATOM|HETATM) lines? Doing it by hand would not be possible in an automated pipeline, for instance.

Best,

-Lane

--

Lane Votapka Ph.D.

Staff Scientist, Amaro lab

UC San Diego

[Lane Votapka]

Aha! I did find a way to instruct parmed to leave out the CRYST line.

For future reference, for the parmed Struct() object you are writing, just set the .box attribute to None

Example:

Struct.box = None

But the question still stands, should pqr2xml ignore those lines? Another possibility would be to incorporate those lines into some kind of box information within the XML file, since sometimes people input periodic box information into simulation software using the CRYST line. It could come in handy if periodic boundary conditions are implemented into Browndye at some future date.

-Lane