Error parsing big files with negative coordinates (concatenated field)

[tubiana]

Hi !

I'm trying to compute an APBS map on a rather big system that contains negatives coordinates under 100A.
Example ;

ATOM  52291  O   ASP O  58     -45.751-100.406  19.252 -0.5819 1.6612

Since there is no space between coord X and coord Y, APBS return me this error :

Valist_readPQR:  Error parsing atom 52291!
Please double check this atom in the pqr file, e.g., make sure there are no concatenated fields.

Is APBS read the pqr file and use a space as separator ? What would be the best workaround according to you ?
I could remove the last decimal of the atom but I just wanted to be sure if you have any better solution :-)

Best regards,
Thibault Tubiana.

I don't know if it is related but i'm on Mac with the last Darwin build.

[sobolevnrm]

Hello. Which version of APBS are you using?

You can pre-process the file using PDB2PQR with the --whitespace option to add spaces between the columns.

[tubiana]

I use the version 3.4.0 but I just tested with a pqr prepared with --whitespace and it works perfectly !
Thank you so much  😃

[sobolevnrm]

Good news; thank you!

[spmorton]

This is a pretty cheezy solution, why not properly parse the valid file?
PDB2PQR reads/writes it just fine per PDB spec but APBS cannot?

[sobolevnrm]

We needed to be able to handle the more general case when coordinates were too large for the official spec.

More generally, mmCIF is a better long-term solution.

[spmorton]

That all may be true, however, for those third party apps like VMD that are expecting the standards based layout, this does not allow them to properly read the PQR file until the non-uniform layout can be handled.