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Elastic network for complex rna strucutres
- ibrahim
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4 years 8 months ago #8178
by ibrahim
Elastic network for complex rna strucutres was created 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
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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- daniloboskovic
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4 years 8 months ago - 4 years 8 months ago #8193
by daniloboskovic
a simple search in the martinize script. There are no definitions for general RNA/DNA hence you might have to experiment and compare.
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: 4 years 8 months ago by daniloboskovic.
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