making cystein bridge with martinizie2

[Byun-jinyoung]

Hello martini users, I have been trying to generate my protein system with cystein bridge. But I encountered the error below:

Traceback (most recent call last):
  File "/home/byun/anaconda3/envs/MD_env/bin/martinize2", line 270, in _cys_argument
    result = float(value)
ValueError: could not convert string to float: 'A/22,A/92'

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

[pckroon]

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)

[Byun-jinyoung]

I used martinize with vermouth 0.7.2 And the error message that I posted was not full messages...

Thank you :)

[pckroon]

Still, you should get the much more intelligible 'The value of the "cys" option must be "auto", "none", or a distance in nanometers.'

[Tsjerk]

This issue has been solved. But I can't readily see when.

[biomolsim]

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.

[pckroon]

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