I am currently trying to monitor the changes that a ligand elicits in the hydrogen bonding pattern of a protein during binding.
I can easily see with the -num flag that the number of internal hydrogen bonds changes throughout the simulation, however would like to identify the specific hbonds. It seems the -hbm flag should be able to do that, however no .xpm file is generated. I seem to get some kind of segmentation fault. This is despite the fact it says the hbmap structure is successfully generated. See below:
Command line:
gmx hbond -f md_0_10_fit.xtc -s md_0_10.tpr -num hb.xvg -hbm
Reading file md_0_10.tpr, VERSION 2020.2 (single precision)
Specify 2 groups to analyze:
Group 0 ( System) has 26828 elements
Group 1 ( Protein) has 2266 elements
Group 2 ( Protein-H) has 1122 elements
Group 3 ( C-alpha) has 141 elements
Group 4 ( Backbone) has 423 elements
Group 5 ( MainChain) has 563 elements
Group 6 ( MainChain+Cb) has 697 elements
Group 7 ( MainChain+H) has 697 elements
Group 8 ( SideChain) has 1569 elements
Group 9 ( SideChain-H) has 559 elements
Group 10 ( Prot-Masses) has 2266 elements
Group 11 ( non-Protein) has 24562 elements
Group 12 ( Other) has 55 elements
Group 13 ( LIG) has 55 elements
Group 14 ( CL) has 3 elements
Group 15 ( Water) has 24504 elements
Group 16 ( SOL) has 24504 elements
Group 17 ( non-Water) has 2324 elements
Group 18 ( Ion) has 3 elements
Group 19 ( LIG) has 55 elements
Group 20 ( CL) has 3 elements
Group 21 ( Water_and_ions) has 24507 elements
Select a group: 1
Selected 1: 'Protein'
Select a group: 1
Selected 1: 'Protein'
Calculating hydrogen bonds in Protein (2266 atoms)
Found 198 donors and 394 acceptors
Making hbmap structure...done.
Reading frame 0 time 0.000
Will do grid-search on 16x15x13 grid, rcut=0.34999999
Last frame 1000 time 9000.000
Found 367 different hydrogen bonds in trajectory
Found 1074 different atom-pairs within hydrogen bonding distance
Merging hbonds with Acceptor and Donor swapped
198/198
- Reduced number of hbonds from 367 to 367
- Reduced number of distances from 1074 to 1074
Average number of hbonds per timeframe 103.381 out of 39006 possible
Segmentation fault: 11
This happens for all of my various protein-ligand simulations. How can I fix this?
Upgrade to version 2020.3 and try again. There was a bug related to matrix processing in various tools that has been fixed.
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