[gmx-users] How to set the inter-chain disulfind bond in martini?

[P C Kroon]

Hi Cheng,

What’s the distance between the two interchain SG atoms? You can either tune the distance used for autodetecting cys bonds, or just specify all of them using the command line. Try `python martinize.py -h`

Peter
PS. The cgmartini.nl forum is also back online, which might be a better medium for these martini specific questions.

From: ZHANG Cheng
Sent: 29 January 2019 16:08
To: gromacs.org_gmx-users
Subject: [gmx-users] How to set the inter-chain disulfind bond in martini?

Dear Martini friends,


My protein has 10 Cys with 5 disulfind bonds in light chain (LC) and heavy chain (HC):
) Interchain disulfide bond: LC214 – HC220
) Intrachain disulfide of LC: LC23 – LC88, LC134 – LC194
) Intrachain disulfide of HC: HC144 – HC200, HC96 – HC22


Using this command will only generate four intrachain disulfide bonds, without the interchain one:
$ python martinize.py -f protein.pdb -o system.top -x protein-CG.pdb -dssp ./dssp-2.0.4-linux-amd64 -p backbone -ff martini22 -cys auto -merge L,H


prompt:
$ INFO       Checking for cystine bridges, based on sulphur (SG) atoms lying closer than 0.2200 nm
$ INFO       Detected SS bridge between ('SG', 'CYS', 23, 'L') and ('SG', 'CYS', 88, 'L') (0.204094 nm)
$ INFO       Detected SS bridge between ('SG', 'CYS', 134, 'L') and ('SG', 'CYS', 194, 'L') (0.204489 nm)
$ INFO       Detected SS bridge between ('SG', 'CYS', 214, 'L') and ('SG', 'CYS', 434, 'H') (0.203603 nm)
$ INFO       Detected SS bridge between ('SG', 'CYS', 358, 'H') and ('SG', 'CYS', 414, 'H') (0.204830 nm)


I can see the four disulfide bonds information is reflected in the [ constraints ] section of "Protein_L+Protein_H.itp" file:
$   45   191      1   0.24000 ; Cys-bonds/special link
$  294   431      1   0.24000 ; Cys-bonds/special link
$  475   947      1   0.24000 ; Cys-bonds/special link
$  778   900      1   0.24000 ; Cys-bonds/special link


So how to also ensure the intactness of the interchain disulfide bond?


You can find my files at
https://github.com/lanselibai/martini/tree/master/20190129_disulfide


Thank you!


Yours sincerely
Cheng
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