Bug #2575
gromacs 2018.2 "gmx rmsf -oq pdb"
Description
In gromacs 2018.2 with the gmx rmsf tool the bfactors pdb outputted by the -oq flag columns are not correctly aligned, leading to gromacs, vmd and pymol misreading the file.
ATOM 8 HA MET A 0 62.005 67.280 72.658 1.00 55.76
ATOM 9 CB MET A 0 60.965 65.570 71.758 1.00 105.42
ATOM 10 HB1 MET A 0 60.015 65.420 71.218 1.00 146.94
ATOM 11 HB2 MET A 0 61.745 65.280 71.038 1.00 112.41
ATOM 12 CG MET A 0 61.015 64.580 72.968 1.00 133.49
ATOM 13 HG1 MET A 0 61.775 64.930 73.688 1.00 180.07
ATOM 14 HG2 MET A 0 60.095 64.710 73.578 1.00 184.69
ATOM 15 SD MET A 0 61.255 62.800 72.588 1.00 139.99
ATOM 16 1MCE MET A 0 59.915 61.570 71.878 1.00 233.45
Associated revisions
History
#1 Updated by Paul Bauer over 1 year ago
Hello, could you add a small example for us to reproduce the exact error? E.g. exact command line input and the corresponding files.
Thanks!
#2 Updated by Owen Vickery over 1 year ago
- File bfac-2018-1.pdb bfac-2018-1.pdb added
- File bfac-2018-2.pdb bfac-2018-2.pdb added
- File pal-wt-pe.tpr pal-wt-pe.tpr added
- File pal-wt-pe.xtc pal-wt-pe.xtc added
Hi
here is a tpr file, and short trajectory and a example pdb from 2018.1 and .2.
The command line is :
echo 1 | gmx rmsf -f pal-wt-pe.xtc -s pal-wt-pe.tpr -oq bfac.pdb
#3 Updated by Paul Bauer over 1 year ago
I confirmed this now. It got caused by b0f4bf1d, even though this should have only ever touched PQR file outputs ...
#4 Updated by Gerrit Code Review Bot over 1 year ago
Gerrit received a related patchset '1' for Issue #2575.
Uploader: Paul Bauer (paul.bauer.q@gmail.com)
Change-Id: gromacs~release-2018~I35c3b99fee81db689df9564c3386edd85e26cbb2
Gerrit URL: https://gerrit.gromacs.org/8109
#5 Updated by Mark Abraham over 1 year ago
- Category set to preprocessing (pdb2gmx,grompp)
- Assignee set to Paul Bauer
- Target version set to 2018.3
#6 Updated by Paul Bauer over 1 year ago
- Status changed from New to Resolved
Applied in changeset c326c8db58761fea4493f0b241225313d2062507.
#7 Updated by Paul Bauer over 1 year ago
- Status changed from Resolved to Closed
#8 Updated by Gerrit Code Review Bot over 1 year ago
Gerrit received a related DRAFT patchset '1' for Issue #2575.
Uploader: Paul Bauer (paul.bauer.q@gmail.com)
Change-Id: gromacs~master~Id841208171da21743a85159242c4c5221adcb309
Gerrit URL: https://gerrit.gromacs.org/8140
Fix bfactor output
The fix for the PQR file output caused the files containing bfactors to
be incorrectly written in this format due to a missing check that has
been added.
Fixes #2575
Change-Id: I35c3b99fee81db689df9564c3386edd85e26cbb2