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martinize request: auto HISH/ASP0/GLU0 support
- johnd
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7 years 7 months ago #5881
by johnd
martinize request: auto HISH/ASP0/GLU0 support was created by johnd
Hi,
This is not a bug or complaint, but just something that I think would be potentially useful in a future martinize update.
In the amino acids itp file ( www.cgmartini.nl/images/parameters/ITP/m..._v2.2_aminoacids.itp ) there are topologies for uncharged ASP (ASP0) and GLU (GLU0) as well as charged HIS (HISH).
If I change HIS to HISH in an aa pdb file, it spits out regular HIS. If I use HIH then it spits out the proper bead types with HIH as the residue name, but it is not the proper name to be recognized in the itp file. It seems like it would be more intuitive to have it detect HISH in the aa pdb and convert that to HISH in the CG pdb, as that is what the residue is called in the itp file
By extension, it would also be helpful to have martinize properly detect when I have changed ASP/GLU to ASP0/GLU0 in an aa pdb, so that the proper bead type/residue name can be automatically added in the CG pdb.
I am aware of the simplicity of going into the protein itp file and manually changing bead types/residue names according to what they are in the amino acid itp file, I just thought this might be helpful in the long run to have added as a feature (or to have an option added to interactively select the charge state of ASP and GLU, as there is for HIS).
Cheers,
John
This is not a bug or complaint, but just something that I think would be potentially useful in a future martinize update.
In the amino acids itp file ( www.cgmartini.nl/images/parameters/ITP/m..._v2.2_aminoacids.itp ) there are topologies for uncharged ASP (ASP0) and GLU (GLU0) as well as charged HIS (HISH).
If I change HIS to HISH in an aa pdb file, it spits out regular HIS. If I use HIH then it spits out the proper bead types with HIH as the residue name, but it is not the proper name to be recognized in the itp file. It seems like it would be more intuitive to have it detect HISH in the aa pdb and convert that to HISH in the CG pdb, as that is what the residue is called in the itp file
By extension, it would also be helpful to have martinize properly detect when I have changed ASP/GLU to ASP0/GLU0 in an aa pdb, so that the proper bead type/residue name can be automatically added in the CG pdb.
I am aware of the simplicity of going into the protein itp file and manually changing bead types/residue names according to what they are in the amino acid itp file, I just thought this might be helpful in the long run to have added as a feature (or to have an option added to interactively select the charge state of ASP and GLU, as there is for HIS).
Cheers,
John
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- danijoo
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7 years 7 months ago #5883
by danijoo
Replied by danijoo on topic martinize request: auto HISH/ASP0/GLU0 support
Yes please! Im currently working on membrane proteins which bear an uncharged Lysine. It would be awesome to not have to do the changes manually after each conversion!
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