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how to "patch" charge residues in martinize.py
- junfeng
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10 years 7 months ago #2076
by junfeng
how to "patch" charge residues in martinize.py was created by junfeng
Hi,
Suppose if GLU200 is neutral, how do I make the coarse-grained GLU200 neutral in the protein topology generated by martinize.py?
I know that I can change it by hand. But there are only two beads representing a neutral GLU(based on the martini_v2.2P_aminoacids.itp), but three beads for charged GLU. Then all the beads index will be shifted...
I tried to rename GLU into GLU0 in pdb, but not working.
Any solution?
Suppose if GLU200 is neutral, how do I make the coarse-grained GLU200 neutral in the protein topology generated by martinize.py?
I know that I can change it by hand. But there are only two beads representing a neutral GLU(based on the martini_v2.2P_aminoacids.itp), but three beads for charged GLU. Then all the beads index will be shifted...
I tried to rename GLU into GLU0 in pdb, but not working.
Any solution?
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- jaakko
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10 years 7 months ago #2106
by jaakko
Replied by jaakko on topic how to "patch" charge residues in martinize.py
Hi junfeng,
Unfortunately martinize can't make the distinction between the two and always creates a charged one. With the polarizable version v2.2P there's the extra dummy bead with the charge that makes it more difficult to change it manually (with other versions the number of beads is the same and you just change the charge). I would try to name the residue in the pdb to something that has just one sidechain bead and then change it manually both at the [ atoms ] section as well as put the right values to the [ bonds ].
Unfortunately martinize can't make the distinction between the two and always creates a charged one. With the polarizable version v2.2P there's the extra dummy bead with the charge that makes it more difficult to change it manually (with other versions the number of beads is the same and you just change the charge). I would try to name the residue in the pdb to something that has just one sidechain bead and then change it manually both at the [ atoms ] section as well as put the right values to the [ bonds ].
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- junfeng
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10 years 7 months ago #2107
by junfeng
Replied by junfeng on topic how to "patch" charge residues in martinize.py
Thanks for the reply.
Can you explain "put the right values to the [ bonds ]"? in more detail?
Can you explain "put the right values to the [ bonds ]"? in more detail?
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- jaakko
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10 years 7 months ago #2108
by jaakko
Replied by jaakko on topic how to "patch" charge residues in martinize.py
If you trick martinize.py to think it is another residue the bond length between backbone and side chain beads might be different. You need to correct that afterwards when you change the residue GLU0.junfeng wrote: Can you explain "put the right values to the [ bonds ]"? in more detail?
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- junfeng
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10 years 7 months ago #2110
by junfeng
Replied by junfeng on topic how to "patch" charge residues in martinize.py
I am sorry. I should be more specific. I am asking what is "right values in the bonds" in the previous message.
For example, I want to use martini 2.2p force field with polarized water and elnedyn. So in martinize.py, I choose elnedyn22p, correct?
Here is what value I should use:
I digged into the "class elnedyn22p" in martinize.py and can find the bond values defined inside the class (under "self.sidechains"). If I use GLU0 for atom types for neutral glutamate and I can still use the same bond value for GLU defined in "self.sidechains", correct?
For example, I want to use martini 2.2p force field with polarized water and elnedyn. So in martinize.py, I choose elnedyn22p, correct?
Here is what value I should use:
I digged into the "class elnedyn22p" in martinize.py and can find the bond values defined inside the class (under "self.sidechains"). If I use GLU0 for atom types for neutral glutamate and I can still use the same bond value for GLU defined in "self.sidechains", correct?
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- jaakko
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10 years 7 months ago #2111
by jaakko
Replied by jaakko on topic how to "patch" charge residues in martinize.py
Yep, you select elnedyn22p in martinize. You can check the correct values for the bond either from the code or more easily from the itp file from the website that you already had a look at. (The v2.2p one with both GLU and GLU0). Then you replace the bond of the "wrong" residue you used to trick martinize with the value for GLU0 (just to be clear it's 0.40 nm and 5000 kJ/mol). It is the same one as for GLU but you needed to call the neutral GLU residues some other residues in the PDB to get the right number of beads and those ones will probably have a different values for the bond. Hope this cleared things.
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- junfeng
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10 years 7 months ago #2112
by junfeng
Replied by junfeng on topic how to "patch" charge residues in martinize.py
Please clarify my confusion here becos the values from the python source code and itp file are different:
In the martini_v2.2P_aminoacids.itp, the bond value for GLU and GLU0 is "0.40 5000". However, in the "class elnedyn22p" from martinize.py, the bond value for GLU is "0.310, 2500". The Elnedyn model claimed to use parameters "read from cg-2.1.dat". on the martini website of Elnedyn, it says "bonded terms defined in original Martini for proteins has been slightly modified to accommodate for the placement of the backbone bead on the Calpha instead on the center-of-mass of the backbone atoms"
Should I use "0.310, 2500" instead of "0.40 5000"?
In the martini_v2.2P_aminoacids.itp, the bond value for GLU and GLU0 is "0.40 5000". However, in the "class elnedyn22p" from martinize.py, the bond value for GLU is "0.310, 2500". The Elnedyn model claimed to use parameters "read from cg-2.1.dat". on the martini website of Elnedyn, it says "bonded terms defined in original Martini for proteins has been slightly modified to accommodate for the placement of the backbone bead on the Calpha instead on the center-of-mass of the backbone atoms"
Should I use "0.310, 2500" instead of "0.40 5000"?
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- Clement
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10 years 7 months ago - 10 years 7 months ago #2128
by Clement
Replied by Clement on topic how to "patch" charge residues in martinize.py
The ElNeDyn force field is a force field in itself; it is slightly different than Martini, and thus labelled as Martini force field as well. Anyway, the point is, you should always use the ElNeDyn parameters when using this option in martinize.py... As you mentioned, the difference are coming from the fact the backbone beads are now moved to the positions of the Cα. Be sure to have the [ constraints ] right for your neutral GLU in you manually modified topology as well! ElNeDyn defines constraints...
Last edit: 10 years 7 months ago by Clement.
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