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How to retain HETATM?
- LucianF
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5 years 1 month ago #8051
by LucianF
How to retain HETATM? was created by LucianF
Dear all,
I am trying to martinize yeast phenylalanine t-RNA(PDB:1ehz), following the tutorial's instruction. After finishing my simulation, I found my structure unstable, and some parts are separated. I think HETATM is the key point because there are other small molecules in the HETATM besides water, which are important in structural stability. Now I want to retain HETATM in the PDB. I read martinize-nucleotide.py and make -hetatm option available. However, it seems unsuccessful because HETATM's residue cannot be recognized by martinize-nucleotide.py. A part of the warning is as follow.
WARNING Skipped unknown residue H2U
WARNING No mapping for coarse graining chain A (Unknown); chain is skipped.
WARNING Skipped unknown residue M2G
WARNING No mapping for coarse graining chain A (Unknown); chain is skipped.
WARNING Skipped unknown residue OMC
I am wondering if I can use martinize-nucleotide.py to retain HETATM, or should I martinize these small molecules one by one manually? What else can I do to get a stable structure?
Tell me if I need to upload other information.
Thanks in advance for any help!
With best wishes.
Lucian
I am trying to martinize yeast phenylalanine t-RNA(PDB:1ehz), following the tutorial's instruction. After finishing my simulation, I found my structure unstable, and some parts are separated. I think HETATM is the key point because there are other small molecules in the HETATM besides water, which are important in structural stability. Now I want to retain HETATM in the PDB. I read martinize-nucleotide.py and make -hetatm option available. However, it seems unsuccessful because HETATM's residue cannot be recognized by martinize-nucleotide.py. A part of the warning is as follow.
WARNING Skipped unknown residue H2U
WARNING No mapping for coarse graining chain A (Unknown); chain is skipped.
WARNING Skipped unknown residue M2G
WARNING No mapping for coarse graining chain A (Unknown); chain is skipped.
WARNING Skipped unknown residue OMC
I am wondering if I can use martinize-nucleotide.py to retain HETATM, or should I martinize these small molecules one by one manually? What else can I do to get a stable structure?
Tell me if I need to upload other information.
Thanks in advance for any help!
With best wishes.
Lucian
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- peterkroon
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5 years 4 weeks ago #8062
by peterkroon
Replied by peterkroon on topic How to retain HETATM?
Hi Lucian,
Option 1) modify martinize-nucleotide.py to also know your residues
Option 2) CG them by hand
Option 3) say "I give up", in which case I'll email you with a link to martinize's successor.
Peter
Option 1) modify martinize-nucleotide.py to also know your residues
Option 2) CG them by hand
Option 3) say "I give up", in which case I'll email you with a link to martinize's successor.
Peter
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5 years 4 weeks ago #8063
by ifaustino
Replied by ifaustino on topic How to retain HETATM?
Hi Lucian,
Thanks for reaching us. I checked the PDB structure and the RNA is full of non-standard residues. Do you really need to include the modified nucleotides or could you 'mutate' them to standard ones? Otherwise I think you would have to parametrize them, which you probably want to avoid.
Cheers,
Ignacio
Thanks for reaching us. I checked the PDB structure and the RNA is full of non-standard residues. Do you really need to include the modified nucleotides or could you 'mutate' them to standard ones? Otherwise I think you would have to parametrize them, which you probably want to avoid.
Cheers,
Ignacio
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- LucianF
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5 years 4 weeks ago #8064
by LucianF
Replied by LucianF on topic How to retain HETATM?
Hi Peter,
Thanks for your help! In fact, I got some progress and also more problems after I post this question on the forum.
To some degree I choose Option 2). I change all the nonstandard nucleotides in HETATM into standard ones in All-Atom PDB file, and martinize-nucleotide.py works successfully. However, here are my questions:
1) Actually, I just changed the resname of nonstandard nucleotides in aa-PDB, for example from 2MG to G, from YYG to G. etc, without changing the number and type of atoms in the PDB file. After applying martinize-nucleotide.py, my coarse-grained output structure is consist of all standard nucleotides, or many standard with few nonstandard? I guess all standard.
2) I read coarse-grained PDB file, and found that A and G have the same composition(BB1 BB2 BB3 SC1 SC2 SC3 SC4). C and U are the same as well(BB1 BB2 BB3 SC1 SC2 SC3). Where are the differences between these two nucleotides in the coarse-grained model?
3) I am a little confused with the elastic network option (stiff/soft). I think this network correspond to RUBBER BAND in ITP file. The truth is, I prepare to use SMD later. Will this kind of band still exist when the RNA secondary structure is destroyed under the tension? I noticed that the stiff network has a cutoff of 1nm. What does cutoff mean here? Does it mean that, for an atom, martinize-nucleotide.py will search other atoms and build RUBBER BAND within 1nm, or it means this kind of bond will disappear when the distance between two atoms beyond 1nm during simulation?
4) In ITP file, RUBBER BAND is type 6 bonds, where is the difference between type 1 and type 6? They have the same expression in GROMACS manual.
If I don't express myself clearly, please let me know.
Thanks again for your help! It means a lot for a rookie!
Best wishes,
Lucian
Thanks for your help! In fact, I got some progress and also more problems after I post this question on the forum.
To some degree I choose Option 2). I change all the nonstandard nucleotides in HETATM into standard ones in All-Atom PDB file, and martinize-nucleotide.py works successfully. However, here are my questions:
1) Actually, I just changed the resname of nonstandard nucleotides in aa-PDB, for example from 2MG to G, from YYG to G. etc, without changing the number and type of atoms in the PDB file. After applying martinize-nucleotide.py, my coarse-grained output structure is consist of all standard nucleotides, or many standard with few nonstandard? I guess all standard.
2) I read coarse-grained PDB file, and found that A and G have the same composition(BB1 BB2 BB3 SC1 SC2 SC3 SC4). C and U are the same as well(BB1 BB2 BB3 SC1 SC2 SC3). Where are the differences between these two nucleotides in the coarse-grained model?
3) I am a little confused with the elastic network option (stiff/soft). I think this network correspond to RUBBER BAND in ITP file. The truth is, I prepare to use SMD later. Will this kind of band still exist when the RNA secondary structure is destroyed under the tension? I noticed that the stiff network has a cutoff of 1nm. What does cutoff mean here? Does it mean that, for an atom, martinize-nucleotide.py will search other atoms and build RUBBER BAND within 1nm, or it means this kind of bond will disappear when the distance between two atoms beyond 1nm during simulation?
4) In ITP file, RUBBER BAND is type 6 bonds, where is the difference between type 1 and type 6? They have the same expression in GROMACS manual.
If I don't express myself clearly, please let me know.
Thanks again for your help! It means a lot for a rookie!
Best wishes,
Lucian
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- LucianF
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5 years 4 weeks ago #8065
by LucianF
Replied by LucianF on topic How to retain HETATM?
Hi Ignacio,
Thanks for your help! Your guidance makes a lot of sense. In fact, I try to do so before you reply, but I got more questions, which have been posted on this topic.
Thanks again! It means a lot for a rookie like me!
Best wishes,
Lucian
Thanks for your help! Your guidance makes a lot of sense. In fact, I try to do so before you reply, but I got more questions, which have been posted on this topic.
Thanks again! It means a lot for a rookie like me!
Best wishes,
Lucian
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- ifaustino
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5 years 4 weeks ago #8066
by ifaustino
Replied by ifaustino on topic How to retain HETATM?
Hi Lucian,
It's good to hear you have done some progress already. I will try to answer your questions.
1) Changing the residue names in the original PDB might not be enough so sometimes you need to delete the heavy-atoms that are not part of the standard residue. That will avoid problems when martinize-nucleotide.py tries to recognize the atoms to build the CG beads on top. Alternatively, try the xleap/tleap program in the Ambertools package to mutate the residues. You would need to first delete all atoms that are not part of the standard residues and xleap will 'fix' them.
2) Although the residues have the same bead names, the bead types are different. If you check the .itp file you will see that, for example, the SC3 in C is not the same as in T. The BB? and SC? notation relates to the bead names but the interactions with other beads depend on the bead types (e.g. TN0, SN2, etc.).
3) Martini does usually a good job if your structure does not have to undergo big conformational changes. If you are planning to manually unfold the RNA, Martini is probably not the best option. The elastic network keeps the structure stable and close to the original conformation. I anticipate that without the elastic network the RNA will distort and the trajectory might be meaningless. If you want some help on the possibilities with the RNA model, you can see the examples in the corresponding article or ask through personal email. Whatever you prefer.
4) The bond type 6 is the default when an elastic network is applied in Martini. This creates an elastic network without exclusions.
Hope this helps and do not hesitate to post your questions.
Ignacio
It's good to hear you have done some progress already. I will try to answer your questions.
1) Changing the residue names in the original PDB might not be enough so sometimes you need to delete the heavy-atoms that are not part of the standard residue. That will avoid problems when martinize-nucleotide.py tries to recognize the atoms to build the CG beads on top. Alternatively, try the xleap/tleap program in the Ambertools package to mutate the residues. You would need to first delete all atoms that are not part of the standard residues and xleap will 'fix' them.
2) Although the residues have the same bead names, the bead types are different. If you check the .itp file you will see that, for example, the SC3 in C is not the same as in T. The BB? and SC? notation relates to the bead names but the interactions with other beads depend on the bead types (e.g. TN0, SN2, etc.).
3) Martini does usually a good job if your structure does not have to undergo big conformational changes. If you are planning to manually unfold the RNA, Martini is probably not the best option. The elastic network keeps the structure stable and close to the original conformation. I anticipate that without the elastic network the RNA will distort and the trajectory might be meaningless. If you want some help on the possibilities with the RNA model, you can see the examples in the corresponding article or ask through personal email. Whatever you prefer.
4) The bond type 6 is the default when an elastic network is applied in Martini. This creates an elastic network without exclusions.
Hope this helps and do not hesitate to post your questions.
Ignacio
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- peterkroon
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5 years 4 weeks ago #8067
by peterkroon
Replied by peterkroon on topic How to retain HETATM?
To continue on 1) martinize(-nucleotide).py recognizes atoms based on their residue name and atom name to know what atoms contributes to what bead. I don't know how it deals with missing or left over atoms. My guess is that it ignores left over atoms, and doesn't complain so long as it finds at least 1 atom for every bead.
If you do a "partial mutation" as you describe the final coordinates you get out will probably be suboptimal, which may have (minor) consequences for the elastic network you get since that depends on the coordinates. The rest of the topology (itp) will be unaffected.
If you do a "partial mutation" as you describe the final coordinates you get out will probably be suboptimal, which may have (minor) consequences for the elastic network you get since that depends on the coordinates. The rest of the topology (itp) will be unaffected.
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