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Bug #3070

make_ndx not recognizing different chains

Added by Cathrine Bergh about 2 months ago. Updated 17 days ago.

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

I wanted to use make_ndx to select a subunit of a pentameric ion channel, but in 2019.3 I still get atoms from all subunits. It seems like the program thinks the whole protein is one chain? The selections I used are in input.txt and the outputs from GROMACS 2019.3 and 2018.4 are in output_201?_?.txt respectively. The selections work fine in 2018.4. Note that in 2019.3 I get 5 times the number of atoms compared to 2018.4.

input.txt (119 Bytes) input.txt Cathrine Bergh, 09/02/2019 11:09 AM
output_2018_4.txt (4.66 KB) output_2018_4.txt Cathrine Bergh, 09/02/2019 11:09 AM
output_2019_3.txt (4.73 KB) output_2019_3.txt Cathrine Bergh, 09/02/2019 11:09 AM
posre_Protein_chain_A.itp (76.8 KB) posre_Protein_chain_A.itp Cathrine Bergh, 09/25/2019 12:32 PM
script.sh (423 Bytes) script.sh Cathrine Bergh, 09/25/2019 12:32 PM
12.ions.pdb (11.5 MB) 12.ions.pdb Cathrine Bergh, 09/25/2019 12:32 PM

Related issues

Related to GROMACS - Bug #3113: Use of read_tps_conf is depecratedNew

Associated revisions

Revision 63c30db7 (diff)
Added by Paul Bauer 17 days ago

Fix chain ID handling in make_ndx

The tool was still using the oldest possible way to read in structure
files, leading to issues with the chain IDs being overwritten and
replaced with the default id.

Fixes #3070
Refs #3113

Change-Id: I25112103a043d0266fe64c7619fe8e4abc56ffa5

History

#1 Updated by Paul Bauer 23 days ago

  • Target version set to 2019.4

should get fixed if possible for the next patch release

#2 Updated by Paul Bauer 23 days ago

@Cathrine, can you also upload sample inputs so I can fully reproduce this to fix the bug?

#3 Updated by Cathrine Bergh 23 days ago

Paul Bauer wrote:

@Cathrine, can you also upload sample inputs so I can fully reproduce this to fix the bug?

Hi! Here's a script you can run with the pdb and itp as input, which should reproduce the bug.

#4 Updated by Paul Bauer 23 days ago

so, reproduced this now and debugging. Was initially introduced when the topology datastructures got a rework

#6 Updated by Paul Bauer 23 days ago

  • Status changed from New to Fix uploaded

#7 Updated by Paul Bauer 17 days ago

  • Related to Bug #3113: Use of read_tps_conf is depecrated added

#8 Updated by Paul Bauer 17 days ago

  • Status changed from Fix uploaded to Resolved

#9 Updated by Paul Bauer 17 days ago

  • Status changed from Resolved to Closed

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