normal Elastic network for complex rna strucutres

  • ibrahim
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1 year 1 month ago #8178 by ibrahim
Dear all,

I am trying to setup martini simulation of RNA-lipid system. The simulations run fine for short (<10 bases) ssRNA with ss-stiff elastic network. However, when I tried with a complex RNA molecule (yeast tRNA Phe), it crashes after few tens of nanoseconds with error "relative constraint deviation", the constrained atoms fall apart. I want to preserve the secondary structure of the molecule hence using ss-stiff elastic network.
Does any one has any suggestions regarding the problem?
Also i am Martinizing the RNA from a PDB crystal structure using the command
"python martinize-nucleotide.py -type ss-stiff -f aa-rna3.pdb -o topology.top -x cg-rna.pdb -p All -pf 1000". In the README file for martinize-nucleotide.py they mention about an option to restrain several strands using the same elastic network for elastic networks of more complicated DNA/RNA structure". Could somebody guide me how to use that option, I think my elastic network is not properly working, as the molecule has both double and single strand regions, and I could only use the ss-stiff network.

Thanks
Ibrahim

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1 year 4 weeks ago - 1 year 4 weeks ago #8193 by daniloboskovic
Replied by daniloboskovic on topic Elastic network for complex rna strucutres
# Write options based on selected topology type.
    options['type'] = options['-type'].value
    if options['type'] == 'ss':
        options['-ff'].setvalue(['martini22nucleic'])
    elif options['type'] == 'ds-stiff':
        options['-ff'].setvalue(['elnedyn22nucleic'])
        lists['merges'].append('A,B')
        options['-eu'].setvalue(['1.0'])
        options['-ef'].setvalue(['500'])
        options['-eb'].setvalue(['BB1,BB2,BB3,SC1,SC2,SC3,SC4'])
    elif options['type'] == 'ds-soft': 
        options['-ff'].setvalue(['elnedyn22nucleic'])
        lists['merges'].append('A,B')
        options['-eu'].setvalue(['1.2'])
        options['-ef'].setvalue(['13'])
        options['-eb'].setvalue(['BB1,BB2,BB3,SC1'])
    elif options['type'] == 'ss-stiff':
        options['-ff'].setvalue(['elnedyn22nucleic'])
        options['-eu'].setvalue(['1.0'])
        options['-ef'].setvalue(['500'])
        options['-eb'].setvalue(['BB1,BB2,BB3,SC1,SC2,SC3,SC4'])
    elif options['type'] == 'ignore':
        pass
    else: 
        logging.error('Undefined topology type. Giving up...')
        sys.exit()

a simple search in the martinize script. There are no definitions for general RNA/DNA hence you might have to experiment and compare.
Last edit: 1 year 4 weeks ago by daniloboskovic.

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