[Apbs-users] pqr file format

[Jianghai Z. <jia...@um...>]

Hi all,

I generated a pqr file using pdb2pqr webserver.  when I ran apbs  
0.5.1, I got the following error.

Parsing input file I-like.pqr.in...
Parsed input file.
Got PQR paths for 1 molecules
Reading PQR-format atom data from I-like.pqr.
Valist_readPQR:  Error parsing ATOM field!
Error while reading molecule from I-like.pqr
Error reading molecules!

My pqr file looks like this.

ATOM      1  N   ASP   109     -61.710-104.919 -76.847 -0.30 1.850
ATOM      2  CA  ASP   109     -63.015-105.565 -76.644  0.21 2.275
ATOM      3  C   ASP   109     -63.850-104.951 -75.482  0.51 2.000
ATOM      4  O   ASP   109     -64.777-105.570 -74.978 -0.51 1.700
ATOM      5  CB  ASP   109     -62.817-107.080 -76.428 -0.28 2.175
ATOM      6  CG  ASP   109     -64.137-107.829 -76.243  0.62 2.000
ATOM      7  OD1 ASP   109     -64.933-107.912 -77.208 -0.76 1.700
ATOM      8  OD2 ASP   109     -64.374-108.330 -75.123 -0.76 1.700
ATOM      9  H2  ASP   109     -61.633-104.125 -76.242  0.33 0.224
ATOM     10  H3  ASP   109     -60.979-105.570 -76.638  0.33 0.224
ATOM     11  H   ASP   109     -61.630-104.622 -77.799  0.33 0.224
ATOM     12  HA  ASP   109     -63.556-105.422 -77.489  0.10 1.320
ATOM     13  HB3 ASP   109     -62.266-107.202 -75.614  0.09 1.320
ATOM     14  HB2 ASP   109     -62.355-107.443 -77.226  0.09 1.320
ATOM     15  N   TYR   110     -63.534-103.724 -75.080 -0.47 1.850
ATOM     16  CA  TYR   110     -64.425-102.974 -74.191  0.07 2.275
ATOM     17  C   TYR   110     -65.844-102.950 -74.766  0.51 2.000

Could anybody give me some suggestions?

Another question.  When I used CHARMM field, pdb2pqr recognized Mg  
ion, but not Ca ion.  What is the atomic radius for Ca?  The Mg  
radius given by CHARMM is 1.185, which is different than the value I  
googled.

Thanks.

Jianghai