Proponation modifications mappings can't be found

[WangLiguo-kyrie]

As in example martinize2 -f 1N6T.pdb -o NKA.top -x NKA_cg.pdb -dssp dssp

atom HD2 in ASP4 was identified as modification [ASP0], but there is unmap warning: WARNING - unmapped-atom - Can't find modification mappings for the modifications ['ASP0'].

Besides, the HD1 in HIS1(modification HSD) wasn't identified.

--version martinize with vermouth 0.7.3

[fgrunewald]

Martinez version 0.7.3 does not correctly identify protonation states. The current development version does given that the neutral amino-acids follow either the Amber or Charmm naming convention.

[WangLiguo-kyrie]

I changed the ASP4 in 1N6T to ASPP format (neutral state in CHARMM naming format): ATOM 53 N ASPPA 4 5.805 0.387 1.403 1.00 0.00 N
ATOM 54 CA ASPPA 4 5.561 0.072 2.800 1.00 0.00 C
ATOM 55 C ASPPA 4 6.009 -1.364 3.081 1.00 0.00 C
ATOM 56 O ASPPA 4 6.236 -1.733 4.232 1.00 0.00 O
ATOM 57 CB ASPPA 4 4.073 0.178 3.137 1.00 0.00 C
ATOM 58 CG ASPPA 4 3.660 1.471 3.844 1.00 0.00 C
ATOM 59 OD1 ASPPA 4 4.335 2.504 3.730 1.00 0.00 O
ATOM 60 OD2 ASPPA 4 2.580 1.388 4.545 1.00 0.00 O
ATOM 61 H ASPPA 4 5.015 0.275 0.800 1.00 0.00 H
ATOM 62 HA ASPPA 4 6.137 0.806 3.364 1.00 0.00 H
ATOM 63 HB2 ASPPA 4 3.499 0.086 2.215 1.00 0.00 H
ATOM 64 HB3 ASPPA 4 3.798 -0.667 3.768 1.00 0.00 H
ATOM 65 HD2 ASPPA 4 2.509 0.480 4.958 1.00 0.00 H

and as in example martinize2 -f 1n6t-pro.pdb -x 1n6t_cg-pro.pdb -o 1n6t-pro.top -ff martini22 warning still existed: WARNING - unmapped-atom - These atoms are not covered by a mapping. Either your mappings don't describe all atoms (bad idea), or, there's no mapping available for all residues. ['53A-ASPP4:N', '54A-ASPP4:CA', '55A-ASPP4:C', '56A-ASPP4:O', '57A-ASPP4:CB', '58A-ASPP4:CG', '59A-ASPP4:OD1', '60A-ASPP4:OD2'] set -maxwarn 1, the result itp file would lack ASPP4 residue

[WangLiguo-kyrie]

Sorry, I didn't realize that "The current development version does" Does the current development version mean not yet released?

[fgrunewald]

The current version means the GitHub development version. So you need to install Martinez from GitHub and it will only work for Martini3 proteins at the moment. I didn't realise you were using martini22

[WangLiguo-kyrie]

I'm using martini3, using martini22 in example was just to stay the same with the force field in tutorial.

I fould the protonation naming in newest martini3 aminoacids.ff and blocks of Universal force field were same(like ASPP), yet the protonation block naming was different (like ASP0). Is this the reason why this development version only work for Martini3 proteins at the moment?

[WangLiguo-kyrie]

I tried the developemnt version. It works. ASPP LSN could be identified and mapped correctly. Thank you!

[fgrunewald]

You're welcome! 😄