Input vs. output hydrogen atom names

HADDOCK
1

Is there any reason that HADDOCK changes the hydrogen atoms names? I am using delenph=false, so both polar and non-polar hydrogen atoms are outputted. The inputs are coming from the Schrodinger Maestro software. You can see that H has been replaced by HN, HB2&HB3 by HB1&HB2, and HG2&HG3 by HG1&HG2.

tleap from Amber doesn’t like the current hydrogen naming scheme from HADDOCK; when comparing with amber parameters files, the hydrogen atom names in the Maestro based input seems to be correct.

It looks like hydrogen atom naming convention should follow Pure Appl Chem 70 :117 (1998)(https://www.cgl.ucsf.edu/chimera/docs/UsersGuide/tutorials/pdbintro.html).

Is there any way to stop HADDOCK from renaming hydrogen atom names?

INPUT:
ATOM 14 N MET 43 34.852 4.355 8.739 1.00 25.71 A N
ATOM 15 CA MET 43 33.763 4.843 9.569 1.00 20.14 A C
ATOM 16 C MET 43 33.810 6.364 9.690 1.00 17.57 A C
ATOM 17 O MET 43 34.859 7.010 9.511 1.00 19.39 A O
ATOM 18 CB MET 43 33.831 4.195 10.960 1.00 19.46 A C
ATOM 19 CG MET 43 33.650 2.713 10.922 1.00 28.91 A C
ATOM 20 SD MET 43 34.188 1.862 12.404 1.00 36.95 A S
ATOM 21 CE MET 43 33.027 0.472 12.369 1.00 39.55 A C
ATOM 22 H MET 43 35.590 3.826 9.182 1.00 0.00 A H
ATOM 23 HA MET 43 32.819 4.562 9.102 1.00 0.00 A H
ATOM 24 HB2 MET 43 34.789 4.431 11.423 1.00 0.00 A H
ATOM 25 HB3 MET 43 33.069 4.636 11.603 1.00 0.00 A H
ATOM 26 HG2 MET 43 32.602 2.482 10.734 1.00 0.00 A H
ATOM 27 HG3 MET 43 34.179 2.307 10.060 1.00 0.00 A H
ATOM 28 HE1 MET 43 33.210 -0.177 13.226 1.00 0.00 A H
ATOM 29 HE2 MET 43 32.006 0.850 12.412 1.00 0.00 A H
ATOM 30 HE3 MET 43 33.166 -0.095 11.448 1.00 0.00 A H

HADDOCK OUTPUT:
ATOM 12 N MET A 43 -28.142 -10.744 -14.057 1.00 10.00 A N
ATOM 13 HN MET A 43 -28.991 -11.230 -14.062 1.00 10.00 A H
ATOM 14 CA MET A 43 -28.141 -9.316 -14.326 1.00 10.00 A C
ATOM 15 HA MET A 43 -27.173 -9.057 -14.726 1.00 10.00 A H
ATOM 16 CB MET A 43 -29.216 -8.964 -15.364 1.00 10.00 A C
ATOM 17 HB1 MET A 43 -29.481 -7.923 -15.255 1.00 10.00 A H
ATOM 18 HB2 MET A 43 -30.092 -9.570 -15.181 1.00 10.00 A H
ATOM 19 CG MET A 43 -28.767 -9.195 -16.802 1.00 10.00 A C
ATOM 20 HG1 MET A 43 -28.472 -10.228 -16.911 1.00 10.00 A H
ATOM 21 HG2 MET A 43 -27.919 -8.560 -17.003 1.00 10.00 A H
ATOM 22 SD MET A 43 -30.051 -8.830 -18.017 1.00 10.00 A S
ATOM 23 CE MET A 43 -29.217 -9.284 -19.539 1.00 10.00 A C
ATOM 24 HE1 MET A 43 -28.841 -10.294 -19.456 1.00 10.00 A H
ATOM 25 HE2 MET A 43 -28.395 -8.607 -19.715 1.00 10.00 A H
ATOM 26 HE3 MET A 43 -29.913 -9.226 -20.363 1.00 10.00 A H
ATOM 27 C MET A 43 -28.365 -8.527 -13.043 1.00 10.00 A C
ATOM 28 O MET A 43 -29.062 -8.985 -12.136 1.00 10.00 A O

2

Yes - because it has to match the force field we are using.

3

Additionally, you can see from the CNS documentation in this link that:

Convention for Hydrogen Names
The hydrogen names follow the scheme that is adopted by the CHARMM all-hydrogen force fields (Brooks et al. 1983). If a different scheme is required, the user can either rename the hydrogens in the topology file or change the molecular structure after it has been created.

4

Thanks for the explanation!

5

HADDOCK does not output NTER hydrogens - HN can be used as H1, but H2 and H3 are still missing. Is there any way to make it do that so the structure is complete for the MD? If this is charmm forcefield, shouldn’t we have them?

6

Hydrogens is something simple to generate via other software if needed.

There will always be differences in naming.

And the default setting is to have uncharged termini (because often what you have in a crystal structure is not the full sequence that was expressed and as such the termini should not be charged).