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 There exists an obsolete atom "SCD" in the code and the output PDB file, which has been replaced by "SCP" or "SCN" atoms in the polarizable aminoacid forcefield definitions.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.
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 There exists an obsolete atom "SCD" in the code and the output PDB file, which has been replaced by "SCP" or "SCN" atoms in the polarizable aminoacid forcefield definitions.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.
Could someone please address this issue? Thank you very much for your kind assistance.