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Issue created by Paul Bauer@acmnpvMaintainer

Editconf mead generates pqr file that can't be used by psize.py tool in APBS - Redmine #2955

Archive from user: Ricardo Ferreira

When using editconf for generating PQR files, there are differences from 2016 version to 2018/2019 versions:

’### GROMACS 2016.5 OUTPUT ###

TITLE     Protein in water
REMARK    THIS IS A SIMULATION BOX
CRYST1  126.566  126.566  166.673  90.00  90.00  90.00 P 1           1
MODEL        1
ATOM      1  N   LYS A  31      57.230  82.330  74.340  0.13  1.57           N
ATOM      2  H1  LYS A  31      57.860  81.680  74.760  0.25  1.20           H
ATOM      3  H2  LYS A  31      57.540  83.220  74.660  0.25  1.20           H
ATOM      4  H3  LYS A  31      57.250  82.220  73.350  0.25  1.20           H

This can be used either with APBS 1.4.2 or 1.5 versions, and also with psize.py tool (provides coarse-grain and fine grids for generating electrostatic maps)

’### psize.py OUTPUT ###

’################# MOLECULE INFO ####################
Number of ATOM entries = 12446
Number of HETATM entries (ignored) = 0
Total charge = 14.580 e
Dimensions = 93.260 x 65.390 x 142.510 A
Center = 59.540 x 61.445 x 82.175 A
Lower corner = 12.910 x 28.750 x 10.920 A
Upper corner = 106.170 x 94.140 x 153.430 A

’############## GENERAL CALCULATION INFO #############
Coarse grid dims = 158.542 x 111.163 x 242.267 A
Fine grid dims = 113.260 x 85.390 x 162.510 A
Num. fine grid pts. = 225 x 161 x 321
Parallel solve required (2217.908 MB >400.000 MB)
Total processors required = 8
Proc. grid = 2 x 2 x 2
Grid pts. on each proc. = 97 x 129 x 129
Fine mesh spacing = 0.703478 x 0.400892 x 0.762958 A
Estimated mem. required for parallel solve = 307.880 MB/proc.
Number of focusing operations = 2

’################# ESTIMATED REQUIREMENTS ####################
Memory per processor = 307.880 MB
Grid storage requirements (ASCII) = 1182.259 MB

*
However, with the new format psize does not work:*

’### GROMACS 2019.2 OUTPUT ###

TITLE     Protein in water
REMARK    THIS IS A SIMULATION BOX
CRYST1  126.566  126.566  166.673  90.00  90.00  90.00 P 1           1
MODEL        1
ATOM   1 N LYS A 31   57.230   82.330   74.340   0.13   1.57
ATOM   2 H1 LYS A 31   57.860   81.680   74.760   0.25   1.20
ATOM   3 H2 LYS A 31   57.540   83.220   74.660   0.25   1.20
ATOM   4 H3 LYS A 31   57.250   82.220   73.350   0.25   1.20

’### psize.py OUTPUT ###

Traceback (most recent call last):
File “/opt/apbs-1.5/share/apbs/tools/manip/psize.py”, line 400, in
if name == “main”: main()
File “/opt/apbs-1.5/share/apbs/tools/manip/psize.py”, line 391, in main
psize.runPsize(filename)
File “/opt/apbs-1.5/share/apbs/tools/manip/psize.py”, line 224, in runPsize
self.parseInput(filename)
File “/opt/apbs-1.5/share/apbs/tools/manip/psize.py”, line 47, in parseInput
self.parseLines(file.readlines())
File “/opt/apbs-1.5/share/apbs/tools/manip/psize.py”, line 59, in parseLines
rad = float(words’[4])
IndexError: list index out of range

However, manually fixing the output with the correct spacing between colums (standard PDB format):

’### GROMACS 2019.2 OUTPUT (MANUALLY FIXED) ###

TITLE     Protein in water
REMARK    THIS IS A SIMULATION BOX
CRYST1  126.566  126.566  166.673  90.00  90.00  90.00 P 1           1
MODEL        1
ATOM      1  N   LYS A  31      57.230  82.330  74.340  0.13  1.57
ATOM      2 H1   LYS A  31      57.860  81.680  74.760  0.25  1.20
ATOM      3 H2   LYS A  31      57.540  83.220  74.660  0.25  1.20
ATOM      4 H3   LYS A  31      57.250  82.220  73.350  0.25  1.20

With this, psize.py works again and provides the correct output.

So it seems that editconf output is wrongly spacing the different columns, and although adherent to the PQR format, it does not seem to comply with PDB standards.

(from redmine: issue id 2955, created on 2019-05-17 by gmxdefault, closed on 2019-05-27)

  • Changesets:
    • Revision f9300d3b by Paul Bauer on 2019-05-24T15:05:06Z:
Fix PQR formatting

Was still broken after the last fix a few months ago.

Fixes #2955

Change-Id: I55b1296918c723654db505d1797114e1358e5aeb