- Posts: 15
Martinize: Charged Histidine incorrectly defined
- peter
- Topic Author
- Offline
- Fresh Boarder
Less
More
2 years 6 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.
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
- Topic Author
- Offline
- Fresh Boarder
Less
More
- Posts: 15
2 years 6 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.
- mason
- Offline
- Fresh Boarder
Less
More
- Posts: 9
2 years 2 months 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.
Time to create page: 0.102 seconds