1. General topics
  3. Tools
  5. Martinize: Charged Histidine incorrectly defined

normal Martinize: Charged Histidine incorrectly defined

  • peter
  • peter's Avatar Topic Author
  • Offline
  • Fresh Boarder
More
2 years 5 months ago #9201 by peter
Martinize: Charged Histidine incorrectly defined was created by peter
Hello everyone,

I came across an issue with "martinize.py" when I ran an MD simulation. Although "martinize.py" is able to detect the HIH residue as an input option, but while writing the ITP file, it is missing the positively charged (+1) D atom from the charged histidine residue.

As a result, there is an inconsistency between the output PDB and ITP files, since the PDB file indeed contains the additional atom too.

Please have a look at this Matini aminoacid topology file . Thank you very much.

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 #9205 by peter
Replied by peter on topic Martinize: Charged Histidine incorrectly defined
The following command was passed to the "martinize.py" module.

python3 martinize.py -f prot.pdb -dssp /usr/bin/dssp -ff elnedyn22p -ef 500 -eu 0.90 -p All -name cg_prot -n cg_prot.ndx -nmap fa_cg_prot.map -x cg_prot.pdb -o cg_prot.top

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

More
2 years 1 month ago #9334 by mason
Replied by mason on topic Martinize: Charged Histidine incorrectly defined
I am experiencing the same issue with generating protonated Histidine using Martinize2. Peter, did you end up fixing this manually?

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

  1. General topics
  3. Tools
  5. Martinize: Charged Histidine incorrectly defined
Time to create page: 0.086 seconds