[apbs-users] Fwd: APBS Error reading molecule

[Abhishek Singha Roy]

Hello,

I need some counsel with an APBS error I am getting.

 

For some reason the attached pqr is giving error on APBS for the attached input file.

Parsing input file lh1_pH4.in...
Parsed input file.
Got paths for 1 molecules
Reading PQR-format atom data from lh1_pH4.pqr.
Valist_readPQR:  Error parsing atom 1!
Error reading molecules!

Please educate me on this. What is wrong with the .pqr file? Also, the version of APBS I have handy is just a bit old. Might that be a problem?

Many thanks

Abhishek Singharoy

[Robert Konecny]

Hi Abishek,

looks like there is no whitespace between your x and y coordinates for
some atoms (since some of your atoms have x and y coordinates > 100A).

You need to rerun pdb2pqr (either command line or the web server) with this
option checked: "Insert whitespaces between atom name and residue name,
between x and y, and between y and z". The generated pqr should be then
readable by APBS.

Best,

Robert

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conversation now. http://goparallel.sourceforge.net/
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[Abhishek Singha Roy]

Many thanks guys! I remade the pqr and APBS is running fine.

Abhishek

[Abhishek Singha Roy]

Many thanks guys! I remade the pqr and APBS is running fine.

Abhishek

On Mon, Mar 23, 2015 at 10:12 AM, Robert Konecny <r...@ucsd.edu> wrote: