Closed Byun-jinyoung closed 2 years ago
Hello hello,
-cys
accepts either 'auto', 'none' or a float (a distance threshold). It no longer allows you to specify specific cysteine bridges. Instead, you should simply add a CONECT record to your pdb with the relevant bond.
It's interesting you don't get a more intelligible error message though. What version of martinize2 are you using? (martinize2 --version
)
I used martinize with vermouth 0.7.2
And the error message that I posted was not full messages...
Thank you :)
Still, you should get the much more intelligible 'The value of the "cys" option must be "auto", "none", or a distance in nanometers.'
This issue has been solved. But I can't readily see when.
Hello Martinize developers,
Instead of adding a CONECT
entry to the .pdb
file, I would prefer to add a line for the desired cysteine-cysteine disulfide linkage to the .itp
file. Any thoughts regarding this? Thanks.
Hi,
not sure what you want to achieve. Martinize2 will produce a CG itp and pdb, which you can adjust (by hand) afterwards as you please. The advantage of adding the SS bond by a conect record is that it makes martinize2 add SS bond to your itp automatically
Hello martini users, I have been trying to generate my protein system with cystein bridge. But I encountered the error below:
I used the command to generate martinized structure
martinize2 -f ${i_crd}.pdb -ff martini3001 -scfix -p backbone -o ${i_crd}-cg.top -x ${i_crd}-cg.pdb -cys A/22,A/92
How can I this problem??? I kindly request your suggestion :)
Thank you