1. General topics
  3. Tools
  5. Martinize: Atom names incorrectly defined

normal Martinize: Atom names incorrectly defined

  • peter
  • peter's Avatar Topic Author
  • Offline
  • Fresh Boarder
More
2 years 5 months ago #9219 by peter
Martinize: Atom names incorrectly defined was created by peter
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 There exists an obsolete atom "SCD" in the code and the output PDB file, which has been replaced by "SCP" or "SCN" atoms in the polarizable aminoacid forcefield definitions.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.

Please Log in or Create an account to join the conversation.

More
2 years 5 months ago #9220 by riccardo
Replied by riccardo on topic Martinize: Atom names incorrectly defined
Hello,
does this apply to martinize or martinize2?

Please Log in or Create an account to join the conversation.

  • peter
  • peter's Avatar Topic Author
  • Offline
  • Fresh Boarder
More
2 years 5 months ago #9223 by peter
Replied by peter on topic Martinize: Atom names incorrectly defined
Thank you very much,

It applies to both "elnedyn22p" and "martini22p" force-field options , which include additional sites for the polarizable and charged amino acid residues as per the updated Martini force-field.

Please Log in or Create an account to join the conversation.

More
2 years 4 months ago #9252 by riccardo
Replied by riccardo on topic Martinize: Atom names incorrectly defined
Sorry for the veeery slow follow-up.

I meant: are you using the "martinize.py" program (bottom of this page:  www.cgmartini.nl/index.php/tools2/proteins-and-bilayers ) or the "martinize2.py" program ( github.com/marrink-lab/vermouth-martinize )?

Please Log in or Create an account to join the conversation.

  • peter
  • peter's Avatar Topic Author
  • Offline
  • Fresh Boarder
More
2 years 4 months ago #9260 by peter
Replied by peter on topic Martinize: Atom names incorrectly defined
I eventually did find the "martinize2" program and it helped with my issue.

Please Log in or Create an account to join the conversation.

  1. General topics
  3. Tools
  5. Martinize: Atom names incorrectly defined
Time to create page: 0.101 seconds