his modificaiton missing data

[csbrasnett]

running eg. martinize2 -f clean.pdb -x cg.pdb -o topol.top -modify HIS:HIS-HP raises an inconsistent data warning about atoms being covered by multiple blocks. Doesn't seem to affect other modifications. Can be fixed by changing the resnames in the input file, but that's not an ideal solution.

Also to note, the HIS-HD modification seems to be wrong, the SC3 bead should become a TN6d, not a as currently is

[fgrunewald]

@csbrasnett could you provide some more information? Are yous sure the modification is detected?

[csbrasnett]

yes, afaict the modification is correctly detected and annotated, but then when it comes to performing it, the residue blocks aren't unique.

It was Liguo who found this first, he'll give some more info too, I couldn't work it out

[fgrunewald]

ohhhhh I think it has something to do with providing it using modify; if you were to just provide the correct pdb file it should work. Or you can use the -mutate flag and put the correctly named residue. That should also work. The modfications actually require the hydrogen atoms to be present.

[WangLiguo-kyrie]

Hi, this the the warning message
'''WARNING - inconsistent-data - These atoms are covered by multiple blocks. This is a bad idea: {'274A-HIS17:HA', '265A-HIS17:C', '279A-HIS17:HE1', '267A-HIS17:CB', '269A-HIS17:ND1', '273A-HIS17:HN', '264A-HIS17:CA', '275A-HIS17:HB2', '276A-HIS17:HB1', '278A-HIS17:HD2', '268A-HIS17:CG', '271A-HIS17:CE1', '272A-HIS17:NE2', '263A-HIS17:N', '266A-HIS17:O', '270A-HIS17:CD2'}. This probably means the following output particles are wrong: {'A-HIS17:SC3', 'A-HIS17:BB', 'A-HIS18:SC1', 'A-HIS17:SC1', 'A-HIS18:SC3', 'A-HIS18:BB', 'A-HIS18:SC2', 'A-HIS17:SC2'}.'''

When we run the command listed above by Chris.

[WangLiguo-kyrie]

ohhhhh I think it has something to do with providing it using modify; if you were to just provide the correct pdb file it should work. Or you can use the -mutate flag and put the correctly named residue. That should also work. The modfications actually require the hydrogen atoms to be present.

yes, when we manually change the resname in pdb from HIS to HSP, it could be recognized although not extra H proton was added in pdb file.

[pckroon]

One of the things I ran into in #631 is that there's something seriously smelly with modifications, and it tends to show for HIS-HP. For now I think the solution is to do -mutate HIS:HSP instead of the modify flag.
I think I know how to fix it, but it requires more mental bandwidth than I have available before my holidays. I'll have a look in February to see if I can bugsquash it.

[WangLiguo-kyrie]

okay, I see. Thanks a lot!
By the way, a small question about the modification definition of "LYS-HZ3". I'm curious why the default charged state of Lys is defined here, whereas other 3 charged residues are not.

[pckroon]

That probably has to do with the fact that modifications can only automatically detect and annotate additional atoms (e.g. protonations). Since there may be missing atoms in the input pdb file, for example because they weren't resolved in xray, missing atoms (e.g. deprotonations) are assumed to be missing/unresolved, rather than omitted on purpose.

[WangLiguo-kyrie]

okay, thanks for the explanation!