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

P C Kroon p.c.kroon at rug.nl
Tue Jan 29 16:17:17 CET 2019


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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