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Bug #2511

Editconf mead generated pqr file didn't follow pqr spec

Added by zhiyi wu 9 months ago. Updated 9 months ago.

Status:
Closed
Priority:
High
Assignee:
-
Category:
-
Target version:
Affected version - extra info:
Affected version:
Difficulty:
uncategorized
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Description

When using editconf to generate pqr files.
gmx editconf -f enmin.tpr -mead system.pqr
The generated pqr file didn't follow the pqr file format specification (https://apbs-pdb2pqr.readthedocs.io/en/latest/formats/pqr.html), where:
  1. The pqr shouldn't contain atom type at the end of the line
  2. There should always be a space separating the columns.

Here is a sample of pqr file.

REMARK The B-factors in this file hold atomic radii
REMARK The occupancy in this file hold atomic charges
TITLE system
REMARK THIS IS A SIMULATION BOX
CRYST1 35.060 34.040 38.990 90.00 90.00 90.00 P 1 1
MODEL 1
ATOM 1 N MET A 1 81.952 52.151 32.219 0.16 1.62 N
ATOM 7335 N MET B 1 30.317 32.933 28.543 0.16 1.62 N
ATOM 7855 N POPEE 474 9.856 33.258 32.940 -0.29 1.65 N
ATOM 10605 N POPEa 496 37.380 63.975 30.931 -0.29 1.65 N
ATOM 13855 N POPE0 522 90.878 72.350 68.454 -0.29 1.65 N
ATOM 15105 N POPE 532 16.405 8.140 68.984 -0.29 1.65 N
TER
ENDMDL

As is shown in the snapshot provided, if the residue name has a length of 4 characters (POPE), there will be no space between residue name and chain id (POPE a) instead of (POPEa).

enmin.tpr (46.1 KB) enmin.tpr zhiyi wu, 05/22/2018 05:21 PM

Associated revisions

Revision b0f4bf1d (diff)
Added by Paul Bauer 9 months ago

Fix PQR file output

PQR files from editconf were always written as fixed format PDB files
with just the field information added. As pointed out in the linked
redmine, this can violate the PQR file standard if the field lengths are
too long, even though the file would still be a valid PDB.

This adds a slightly different form of the writeout that has a flexible,
PQR conform format.

Fixes #2511

Change-Id: I626380b642a0214970753da289e9c969ce411ea7

History

#1 Updated by Gerrit Code Review Bot 9 months ago

Gerrit received a related patchset '1' for Issue #2511.
Uploader: Paul Bauer ()
Change-Id: gromacs~release-2018~I626380b642a0214970753da289e9c969ce411ea7
Gerrit URL: https://gerrit.gromacs.org/7929

#2 Updated by Mark Abraham 9 months ago

Can you please share the .tpr file, so we can perhaps agree on how the output should look if/when we fix editconf?

#3 Updated by Mark Abraham 9 months ago

  • Status changed from New to Fix uploaded

#4 Updated by zhiyi wu 9 months ago

Mark Abraham wrote:

Can you please share the .tpr file, so we can perhaps agree on how the output should look if/when we fix editconf?

Here is a sample tpr file contain two POPE molecules.
If "gmx editconf -f enmin.tpr -mead system.pqr" was run, the output pqr file will be

REMARK The B-factors in this file hold atomic radii
REMARK The occupancy in this file hold atomic charges
TITLE GkApcT YneM POPE POPG in water
REMARK THIS IS A SIMULATION BOX
CRYST1 109.329 90.329 91.654 90.00 90.00 90.00 P 1 1
MODEL 1
ATOM 1 N POPEA 1 14.430 46.000 29.240 -0.29 1.65 N
...
ATOM 250 H16Z POPEB 2 100.140 5.340 54.660 0.02 1.10 H
TER
ENDMDL

The suggested output which adheres to the pqr spec will be:

REMARK The B-factors in this file hold atomic radii
REMARK The occupancy in this file hold atomic charges
TITLE GkApcT YneM POPE POPG in water
REMARK THIS IS A SIMULATION BOX
CRYST1 109.329 90.329 91.654 90.00 90.00 90.00 P 1 1
MODEL 1
ATOM 1 N POPE A 1 14.430 46.000 29.240 -0.29 1.65
...
ATOM 250 H16Z POPE B 2 100.140 5.340 54.660 0.02 1.10
TER
ENDMDL

#5 Updated by Paul Bauer 9 months ago

  • Status changed from Fix uploaded to Resolved

#6 Updated by Mark Abraham 9 months ago

  • Status changed from Resolved to Closed
  • Target version set to 2018.2

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