[apbs-users] A bug of APBS in reading PQR file

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LI An-Bang

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May 3, 2015, 10:05:05 PM5/3/15
to apbs-users
Hi, developers of APBS,

Here I report a bug of APBS in reading PQR file.

I have some PQR files in ambPQR format. When I run APBS calculation, I got the following error information:

Parsing input file 4ull.in...
Parsed input file.
Got paths for 1 molecules
Reading PQR-format atom data from 4ull.pqr.
Valist_readPDB:  Unable to parse serial token (radii) as int!
Valist_readPDB:  Error while parsing serial!
Valist_readPDB:  Can't find x!
Valist_readPQR:  Error parsing atom -1728265984!

After checking the PQR file, I found that the reason comes from the REMARK lines of the PQR file:

REMARK  atom radii in columns 55-62
REMARK  atom charges in columns 63-70

The lines begin with keyword "REMARK" and follow with word "atom". APBS recognize the lines as  atom information lines with keyword "ATOM". And thus the error occurs. I deleted the "atom" word in the lines and the error disapeared.

Please check this.

Best regards,, 
Anbang

------------------
LI AnBang
Physics Department, Central China Normal University, China
 

Baker, Nathan

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May 3, 2015, 11:19:58 PM5/3/15
to LI An-Bang, apbs-users, Jurrus, Elizabeth R, Star, Keith

Hello –

 

Please provide an example of the PQR file so we can debug.

 

Thank you,

 

--

Nathan Baker

Laboratory Fellow and Technical Group Manager

Applied Statistics and Computational Modeling Group

Pacific Northwest National Laboratory

+1-509-375-3997

http://goo.gl/U9xu4t

LI An-Bang

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May 3, 2015, 11:36:03 PM5/3/15
to Baker, Nathan, apbs-users, Jurrus, Elizabeth R, Star, Keith
Hi,

Just put any lines containing "REMARK  atom " in the PQR file, the error will occur.

Attached an example file.

Best,
Anbang

------------------ Original ------------------
From:  "Baker, Nathan";<Nathan...@pnnl.gov>;
Date:  Mon, May 4, 2015 11:19 AM
To:  "LI An-Bang"<anba...@qq.com>; "apbs-users"<apbs-...@lists.sourceforge.net>;
Cc:  "Jurrus, Elizabeth R"<Elizabet...@pnnl.gov>; "Star, Keith"<ke...@pnnl.gov>;
Subject:  RE: [apbs-users] A bug of APBS in reading PQR file
1ajj.pqr

Baker, Nathan

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May 4, 2015, 8:30:26 PM5/4/15
to LI An-Bang, apbs-users, Jurrus, Elizabeth R, Star, Keith

Hello –

 

Thank you for the additional information.  Liz/Keith, can you please file this issue on GitHub and investigate a fix?

 

Thanks,

Star, Keith

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May 4, 2015, 9:22:17 PM5/4/15
to Baker, Nathan, LI An-Bang, apbs-users, Jurrus, Elizabeth R
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