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elastic network between two subunits
- ruoxu
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9 years 10 months ago #3907
by ruoxu
elastic network between two subunits was created by ruoxu
Hi All:
I am trying to use elastic network to simulate proteins, and in my case, I need to incorporate some elastic network between two protein subunits, however, when I use Martini.py to generate the the topology files, I always get several files. Each files is for one subunit, and elastic network is only applied for each subunit, not between these subunits.
I think this is because I used chain numbers in my initial PDB file. So I am thinking to remove these chain numbers. Will this help me to generate elastic networks between subunits? Or it will introduce un-expected (and wrong) bonded interactions between the protein subunits?
Are there any way to apply elastic network between different protein subunits?
Thanks,
RuoXu Gu
I am trying to use elastic network to simulate proteins, and in my case, I need to incorporate some elastic network between two protein subunits, however, when I use Martini.py to generate the the topology files, I always get several files. Each files is for one subunit, and elastic network is only applied for each subunit, not between these subunits.
I think this is because I used chain numbers in my initial PDB file. So I am thinking to remove these chain numbers. Will this help me to generate elastic networks between subunits? Or it will introduce un-expected (and wrong) bonded interactions between the protein subunits?
Are there any way to apply elastic network between different protein subunits?
Thanks,
RuoXu Gu
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- xavier
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9 years 8 months ago #4016
by xavier
Replied by xavier on topic elastic network between two subunits
In Martinize you have the option to merge chains (-merge). This might allow you to generate bonds between chains without more efforts.
If it does not generate bonds between chains you'll have to generate a set of bonds by hand removing the chain identifier and then include the interchain bonds into a topology where the two chains are merged. This should be quite trivial.
Note that to have bonds between chains you have to have them merged.
If it does not generate bonds between chains you'll have to generate a set of bonds by hand removing the chain identifier and then include the interchain bonds into a topology where the two chains are merged. This should be quite trivial.
Note that to have bonds between chains you have to have them merged.
ruoxu wrote: Hi All:
I am trying to use elastic network to simulate proteins, and in my case, I need to incorporate some elastic network between two protein subunits, however, when I use Martini.py to generate the the topology files, I always get several files. Each files is for one subunit, and elastic network is only applied for each subunit, not between these subunits.
I think this is because I used chain numbers in my initial PDB file. So I am thinking to remove these chain numbers. Will this help me to generate elastic networks between subunits? Or it will introduce un-expected (and wrong) bonded interactions between the protein subunits?
Are there any way to apply elastic network between different protein subunits?
Thanks,
RuoXu Gu
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- Luca
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8 years 6 months ago #4981
by Luca
Can i use martinize to create elnedyn restraints with coarse grain proteins? or should i start from a pdb of the 2 protein and then convert them with martinize to generate those restraints with -merge?
second question. Can i change restraints from quaternary structure to the single protein restraint?
Like change the file with restraints with another file with the single protein restraints. does it work?
thanks
Replied by Luca on topic elastic network between two subunits
xavier wrote: In Martinize you have the option to merge chains (-merge). This might allow you to generate bonds between chains without more efforts.
If it does not generate bonds between chains you'll have to generate a set of bonds by hand removing the chain identifier and then include the interchain bonds into a topology where the two chains are merged. This should be quite trivial.
Note that to have bonds between chains you have to have them merged.
ruoxu wrote: Hi All:
I am trying to use elastic network to simulate proteins, and in my case, I need to incorporate some elastic network between two protein subunits, however, when I use Martini.py to generate the the topology files, I always get several files. Each files is for one subunit, and elastic network is only applied for each subunit, not between these subunits.
I think this is because I used chain numbers in my initial PDB file. So I am thinking to remove these chain numbers. Will this help me to generate elastic networks between subunits? Or it will introduce un-expected (and wrong) bonded interactions between the protein subunits?
Are there any way to apply elastic network between different protein subunits?
Thanks,
RuoXu Gu
Can i use martinize to create elnedyn restraints with coarse grain proteins? or should i start from a pdb of the 2 protein and then convert them with martinize to generate those restraints with -merge?
second question. Can i change restraints from quaternary structure to the single protein restraint?
Like change the file with restraints with another file with the single protein restraints. does it work?
thanks
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