Martinize: Atom names incorrectly defined

[biomolsim]

Cross-posting from the Martini forum

Hello everyone,

The sidechain atom names for most polar and charged residues have been incorrectly defined in the code segment that writes the PDB file. There exists an obsolete atom "SCD" in the code and the output PDB file, which has been replaced by "SCP" or "SCN" atoms in the polarizable aminoacid forcefield definitions. The ITP file gets correctly written though, and hence there is a mismatch between the atom names in the PDB and the ITP files.

#PDB file

ATOM     12  BB  SER X  76     106.618 144.399 144.447  1.00  2.00           B 
ATOM     13  SC1 SER X  76     106.727 143.121 145.975  1.00  2.00           S 
ATOM     14  SCD SER X  76     106.721 143.010 146.060  1.00  2.00           S 
ATOM     15  SCD SER X  76     106.732 143.232 145.890  1.00  2.00           S 

#ITP file

   12    N0    12   SER    BB    27  0.0000 ; H
   13    N0    12   SER   SC1    28  0.0000  0.0000 ; H
   14     D    12   SER   SCP    29  0.4000 36.0000 ; H
   15     D    12   SER   SCN    30 -0.4000 36.0000 ; H

Could someone please address this issue? Thank you very much for your kind assistance.