Issues generating hbmap.xpm file from gromacs hbond module, using -xpm flag?
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14 months ago

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. Its 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. This happens for all of my various protein-ligand simulations. How can I fix this. 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

gromacs hbmap xpm segmentation fault gmx hbond • 450 views
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