[gmx-users] Parametrization using MARTINI 2.2P force field

[James Starlight]

Dear Gromacs users!

I have faced with the problem of the ussage of martini force field for
the parametrization of water soluble proteins. Particularly for my
cased there is a problem with the polarizable martini 2 2p force field

while execulting
python martinize.py -f 5AXS_proc_fix.pdb -x test.pdb -o topol_cg.top
-dssp /projects/clouddyn/Software/dssp -p backbone -ff martini22p

I obtained

WARNING    Bead names of charges in sidechains differ between
.top/.itp and .pdb.
WARNING    Using names in topology, as Gromacs does, gives the correct result.



and then grompp gave me error regarding mesmatched atoms in my pdb and itp


Excluding 1 bonded neighbours molecule type 'Protein_A'
Warning: atom name 5 in topol_cg.top and test-CG.gro does not match (SCP - SCD)
Warning: atom name 6 in topol_cg.top and test-CG.gro does not match (SCN - SCD)
Warning: atom name 18 in topol_cg.top and test-CG.gro does not match (SCP - SCD)
Warning: atom name 21 in topol_cg.top and test-CG.gro does not match (SCP - SCD)
Warning: atom name 22 in topol_cg.top and test-CG.gro does not match (SCN - SCD)
Warning: atom name 27 in topol_cg.top and test-CG.gro does not match (SCP - SCD)
Warning: atom name 28 in topol_cg.top and test-CG.gro does not match (SCN - SCD)
Warning: atom name 33 in topol_cg.top and test-CG.gro does not match (SCP - SCD)
Warning: atom name 36 in topol_cg.top and test-CG.gro does not match (SCP - SCD)
Warning: atom name 37 in topol_cg.top and test-CG.gro does not match (SCN - SCD)
Warning: atom name 42 in topol_cg.top and test-CG.gro does not match (SCP - SCD)
Warning: atom name 43 in topol_cg.top and test-CG.gro does not match (SCN - SCD)
Warning: atom name 48 in topol_cg.top and test-CG.gro does not match (SCN - SCD)
Warning: atom name 53 in topol_cg.top and test-CG.gro does not match (SCN - SCD)
Warning: atom name 58 in topol_cg.top and test-CG.gro does not match (SCP - SCD)
Warning: atom name 59 in topol_cg.top and test-CG.gro does not match (SCN - SCD)
Warning: atom name 62 in topol_cg.top and test-CG.gro does not match (SCN - SCD)
Warning: atom name 65 in topol_cg.top and test-CG.gro does not match (SCP - SCD)
Warning: atom name 66 in topol_cg.top and test-CG.gro does not match (SCN - SCD)
Warning: atom name 71 in topol_cg.top and test-CG.gro does not match (SCN - SCD)
(more than 20 non-matching atom names)

WARNING 1 [file topol_cg.top, line 14]:
  58 non-matching atom names
  atom names from topol_cg.top will be used
  atom names from test-CG.gro will be ignored


its stange that I have not such problem using martini2.1p force field
or mertini 2.2 (not polarizable version of 2.2p),

How I could solve the issue?

Thanks for help!!

James