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

[ZHANG Cheng]

Dear Peter,


Thank you, I find the answer now. Sorry I was using a pdb that the SS length is too long to form the SS bond. After changing to a correct one, I got the solution.


I think, if we have more than one chain, we MUST use "-merge" option, so that the interchain SS bond can shown in the generated itp file.


If "-merge" is missing, only the intra-chain SS bonds are shown in the individual itp files.


So happy to see the martini forum come back!


Yours sincerely
Cheng 




------------------ Original ------------------
From:  "ZHANG Cheng"<272699575 at qq.com>;
Date:  Tue, Jan 29, 2019 11:03 PM
To:  "gromacs.org_gmx-users"<gromacs.org_gmx-users at maillist.sys.kth.se>;

Subject:  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